[3D-TOF MR-angiography with high spatial resolution for surgical planning in insular lobe gliomas].

PubMed

Bykanov, A E; Pitskhelauri, D I; Pronin, I N; Tonoyan, A S; Kornienko, V N; Zakharova, N E; Turkin, A M; Sanikidze, A Z; Shkarubo, M A; Shkatova, A M; Shults, E I

2015-01-01

Despite the obvious progress in modern neurosurgery, surgery for glial tumors of the insular lobe is often associated with a high risk of postoperative neurological deficit, which is primarily caused by damage to perforating arteries of the M1 segment of the middle cerebral artery. The work is aimed at evaluating the effectiveness of high resolution time-of-flight (3D-TOF) MR angiography in imaging of medial and lateral lenticulostriate arteries and determining their relationship to tumor edge in patients with gliomas of the insula. 3D-TOF MR angiography data were analyzed in 20 patients with primarily diagnosed cerebral gliomas involving the insula. All patients underwent non-contrast enhanced 3D-TOF MR angiography. In 6 cases, 3D-TOF MRA was performed before and after contrast enhancement. 3D-TOF angiography before intravenous contrast injection was capable of visualizing the medial lenticulostriate arteries in 19 patients (95% of all cases) and lateral lenticulostriate arteries in 18 patients (90% of all cases). Contrast-enhanced 3D-TOF angiography allows for better visualization of both the proximal and distal segments of lenticulostriate arteries. Three variants of relationship between the tumor and lenticulostriate arteries were identified. Variant I: the tumor grew over the arteries without their displacement in 2 cases (10% of the total number of observations); variant II: the tumor caused medial displacement of arteries without growing over them in 11 cases (55% of the total number of observations); variant III: the tumor partially grew over and displaced arteries in 2 cases (10%). In 25% of cases (5 patients), tumor was poorly visualized on 3D-TOF MR angiograms because their signal characteristics did not differ from those of the medulla (tumor tissue was T1 isointense). As a result, it was impossible to determine the relationship between the tumor and lenticulostriate arteries. High spatial resolution time-of-flight MR angiography can be recommended for preoperative imaging of lenticulostriate arteries to plan the extent of neurosurgical resection in patients with glial tumors of the insular lobe.

Analogous Three-Dimensional Constructive Interference in Steady State Sequences Enhance the Utility of Three-Dimensional Time of Flight Magnetic Resonance Angiography in Delineating Lenticulostriate Arteries in Insular Gliomas: Evidence from a Prospective Clinicoradiologic Analysis of 48 Patients.

PubMed

Rao, Arun S; Thakar, Sumit; Sai Kiran, Narayanam Anantha; Aryan, Saritha; Mohan, Dilip; Hegde, Alangar S

2018-01-01

Three-dimensional (3D) time of flight (TOF) imaging is the current gold standard for noninvasive, preoperative localization of lenticulostriate arteries (LSAs) in insular gliomas; however, the utility of this modality depends on tumor intensity. Over a 3-year period, 48 consecutive patients with insular gliomas were prospectively evaluated. Location of LSAs and their relationship with the tumor were determined using a combination of contrast-enhanced coronal 3D TOF magnetic resonance angiography and coronal 3D constructive interference in steady state (CISS) sequences. These findings were analyzed with respect to extent of tumor resection and early postoperative motor outcome. Tumor was clearly visualized in 29 (60.4%) patients with T1-hypointense tumors using 3D TOF and in all patients using CISS sequences. Using combined 3D TOF and CISS, LSA-tumor interface was well seen in 47 patients, including all patients with T1-heterointense or T1-isointense tumors. Extent of resection was higher in the LSA-pushed group compared with the LSA-encased group. In the LSA-encased group, 6 (12.5%) patients developed postoperative hemiparesis; 2 (4.2%) cases were attributed to LSA injury. Contrast-enhanced 3D TOF can delineate LSAs in almost all insular gliomas but is limited in identifying the LSA-tumor interface. This limitation can be overcome by addition of analogous CISS sequences that delineate the LSA-tumor interface regardless of tumor intensity. Combined 3D TOF and 3D CISS is a useful tool for surgical planning and safer resections of insular tumors and may have added surgical relevance when included as an intraoperative adjunct. Copyright © 2017 Elsevier Inc. All rights reserved.

Diagnostic value of 3D time-of-flight MRA in trigeminal neuralgia.

PubMed

Cai, Jing; Xin, Zhen-Xue; Zhang, Yu-Qiang; Sun, Jie; Lu, Ji-Liang; Xie, Feng

2015-08-01

The aim of this meta-analysis was to evaluate the diagnostic value of 3D time-of-flight magnetic resonance angiography (3D-TOF-MRA) in trigeminal neuralgia (TN). Relevant studies were identified by computerized database searches supplemented by manual search strategies. The studies were included in accordance with stringent inclusion and exclusion criteria. Following a multistep screening process, high quality studies related to the diagnostic value of 3D-TOF-MRA in TN were selected for meta-analysis. Statistical analyses were conducted using Statistical Analysis Software (version 8.2; SAS Institute, Cary, NC, USA) and Meta Disc (version 1.4; Unit of Clinical Biostatistics, Ramon y Cajal Hospital, Madrid, Spain). For the present meta-analysis, we initially retrieved 95 studies from database searches. A total of 13 studies were eventually enrolled containing a combined total of 1084 TN patients. The meta-analysis results demonstrated that the sensitivity and specificity of the diagnostic value of 3D-TOF-MRA in TN were 95% (95% confidence interval [CI] 0.93-0.96) and 77% (95% CI 0.66-0.86), respectively. The pooled positive likelihood ratio and negative likelihood ratio were 2.72 (95% CI 1.81-4.09) and 0.08 (95% CI 0.06-0.12), respectively. The pooled diagnostic odds ratio of 3D-TOF-MRA in TN was 52.92 (95% CI 26.39-106.11), and the corresponding area under the curve in the summary receiver operating characteristic curve based on the 3D-TOF-MRA diagnostic image of observers was 0.9695 (standard error 0.0165). Our results suggest that 3D-TOF-MRA has excellent sensitivity and specificity as a diagnostic tool for TN, and that it can accurately identify neurovascular compression in TN patients. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of the inflow zone of unruptured cerebral aneurysms: comparison of 4D flow MRI and 3D TOF MRA data.

PubMed

Futami, K; Sano, H; Misaki, K; Nakada, M; Ueda, F; Hamada, J

2014-07-01

The hemodynamics of the inflow zone of cerebral aneurysms may be a key factor in coil compaction and recanalization after endovascular coil embolization. We performed 4D flow MR imaging in conjunction with 3D TOF MRA and compared their ability to identify the inflow zone of unruptured cerebral aneurysms. This series comprised 50 unruptured saccular cerebral aneurysms in 44 patients. Transluminal color-coded 3D MRA images were created by selecting the signal-intensity ranges on 3D TOF MRA images that corresponded with both the luminal margin and the putative inflow. 4D flow MR imaging demonstrated the inflow zone and yielded inflow velocity profiles for all 50 aneurysms. In 18 of 24 lateral-projection aneurysms (75%), the inflow zone was located distally on the aneurysmal neck. The maximum inflow velocity ranged from 285 to 922 mm/s. On 4D flow MR imaging and transluminal color-coded 3D MRA studies, the inflow zone of 32 aneurysms (64%) was at a similar location. In 91% of aneurysms whose neck section plane angle was <30° with respect to the imaging section direction on 3D TOF MRA, depiction of the inflow zone was similar on transluminal color-coded 3D MRA and 4D flow MR images. 4D flow MR imaging can demonstrate the inflow zone and provide inflow velocity profiles. In aneurysms whose angle of the neck-section plane is obtuse vis-a-vis the imaging section on 3D TOF MRA scans, transluminal color-coded 3D MRA may depict the inflow zone reliably. © 2014 by American Journal of Neuroradiology.

Magnetic Resonance Angiography in the Diagnosis of Cerebral Arteriovenous Malformation and Dural Arteriovenous Fistulas: Comparison of Time-Resolved Magnetic Resonance Angiography and Three Dimensional Time-of-Flight Magnetic Resonance Angiography

PubMed Central

Cheng, Yu-Ching; Chen, Hung-Chieh; Wu, Chen-Hao; Wu, Yi-Ying; Sun, Ming-His; Chen, Wen-Hsien; Chai, Jyh-Wen; Chi-Chang Chen, Clayton

2016-01-01

Background Traditional digital subtraction angiography (DSA) is currently the gold standard diagnostic method for the diagnosis and evaluation of cerebral arteriovenous malformation (AVM) and dural arteriovenous fistulas (dAVF). Objectives The aim of this study was to analyze different less invasive magnetic resonance angiography (MRA) images, time-resolved MRA (TR-MRA) and three-dimensional time-of-flight MRA (3D TOF MRA) to identify their diagnostic accuracy and to determine which approach is most similar to DSA. Patients and Methods A total of 41 patients with AVM and dAVF at their initial evaluation or follow-up after treatment were recruited in this study. We applied time-resolved angiography using keyhole (4D-TRAK) MRA to perform TR-MRA and 3D TOF MRA examinations simultaneously followed by DSA, which was considered as a standard reference. Two experienced neuroradiologists reviewed the images to compare the diagnostic accuracy, arterial feeder and venous drainage between these two MRA images. Inter-observer agreement for different MRA images was assessed by Kappa coefficient and the differences of diagnostic accuracy between MRA images were evaluated by the Wilcoxon rank sum test. Results Almost all vascular lesions (92.68%) were correctly diagnosed using 4D-TRAK MRA. However, 3D TOF MRA only diagnosed 26 patients (63.41%) accurately. There were statistically significant differences regarding lesion diagnostic accuracy (P = 0.008) and venous drainage identification (P < 0.0001) between 4D-TRAK MRA and 3D TOF MRA. The results indicate that 4D-TRAK MRA is superior to 3D TOF MRA in the assessment of lesions. Conclusion Compared with 3D TOF MRA, 4D-TRAK MRA proved to be a more reliable screening modality and follow-up method for the diagnosis of cerebral AVM and dAVF. PMID:27679690

A pitfall of the volume rendering method with 3D time-of-flight MRA: a case of a branching vessel at the aneurysm neck.

PubMed

Goto, Masami; Kunimatsu, Akira; Shojima, Masaaki; Abe, Osamu; Aoki, Shigeki; Hayashi, Naoto; Mori, Harushi; Ino, Kenji; Yano, Keiichi; Saito, Nobuhito; Ohtomo, Kuni

2013-03-25

We present a case in which the origin of the branching vessel at the aneurysm neck was observed at the wrong place on the volume rendering method (VR) with 3D time-of-flight MRA (3D-TOF-MRA) with 3-Tesla MR system. In 3D-TOF-MRA, it is often difficult to observe the origin of the branching vessel, but it is unusual for it to be observed in the wrong place. In the planning of interventional treatment and surgical procedures, false recognition, as in the unique case in the present report, is a serious problem. Decisions based only on VR with 3D-TOF-MRA can be a cause of suboptimal selection in clinical treatment.

Follow-up of intracranial aneurysms treated by flow diverter: comparison of three-dimensional time-of-flight MR angiography (3D-TOF-MRA) and contrast-enhanced MR angiography (CE-MRA) sequences with digital subtraction angiography as the gold standard.

PubMed

Attali, Jonathan; Benaissa, Azzedine; Soize, Sébastien; Kadziolka, Krzysztof; Portefaix, Christophe; Pierot, Laurent

2016-01-01

Follow-up of intracranial aneurysms treated by flow diverter with MRI is complicated by imaging artifacts produced by these devices. This study compares the diagnostic accuracy of three-dimensional time-of-flight MR angiography (3D-TOF-MRA) and contrast-enhanced MRA (CE-MRA) at 3 T for the evaluation of aneurysm occlusion and parent artery patency after flow diversion treatment, with digital subtraction angiography (DSA) as the gold standard. Patients treated with flow diverters between January 2009 and January 2013 followed by MRA at 3 T (3D-TOF-MRA and CE-MRA) and DSA within a 48 h period were included in a prospective single-center study. Aneurysm occlusion was assessed with full and simplified Montreal scales and parent artery patency with three-grade and two-grade scales. Twenty-two patients harboring 23 treated aneurysms were included. Interobserver agreement using simplified scales for occlusion (Montreal) and parent artery patency were higher for DSA (0.88 and 0.61) and CE-MRA (0.74 and 0.55) than for 3D-TOF-MRA (0.51 and 0.02). Intermodality agreement was higher for CE-MRA (0.88 and 0.32) than for 3D-TOF-MRA (0.59 and 0.11). CE-MRA yielded better accuracy than 3D-TOF-MRA for aneurysm remnant detection (sensitivity 83% vs 50%; specificity 100% vs 100%) and for the status of the parent artery (specificity 63% vs 32%; sensitivity 100% vs 100%). At 3 T, CE-MRA is superior to 3D-TOF-MRA for the evaluation of aneurysm occlusion and parent artery patency after flow diversion treatment. However, intraluminal evaluation remains difficult with MRA regardless of the sequence used. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Comparison of 3D computer-aided with manual cerebral aneurysm measurements in different imaging modalities.

PubMed

Groth, M; Forkert, N D; Buhk, J H; Schoenfeld, M; Goebell, E; Fiehler, J

2013-02-01

To compare intra- and inter-observer reliability of aneurysm measurements obtained by a 3D computer-aided technique with standard manual aneurysm measurements in different imaging modalities. A total of 21 patients with 29 cerebral aneurysms were studied. All patients underwent digital subtraction angiography (DSA), contrast-enhanced (CE-MRA) and time-of-flight magnetic resonance angiography (TOF-MRA). Aneurysm neck and depth diameters were manually measured by two observers in each modality. Additionally, semi-automatic computer-aided diameter measurements were performed using 3D vessel surface models derived from CE- (CE-com) and TOF-MRA (TOF-com) datasets. Bland-Altman analysis (BA) and intra-class correlation coefficient (ICC) were used to evaluate intra- and inter-observer agreement. BA revealed the narrowest relative limits of intra- and inter-observer agreement for aneurysm neck and depth diameters obtained by TOF-com (ranging between ±5.3 % and ±28.3 %) and CE-com (ranging between ±23.3 % and ±38.1 %). Direct measurements in DSA, TOF-MRA and CE-MRA showed considerably wider limits of agreement. The highest ICCs were observed for TOF-com and CE-com (ICC values, 0.92 or higher for intra- as well as inter-observer reliability). Computer-aided aneurysm measurement in 3D offers improved intra- and inter-observer reliability and a reproducible parameter extraction, which may be used in clinical routine and as objective surrogate end-points in clinical trials.

A comparative study of magnetic resonance venography techniques for the evaluation of the internal jugular veins in multiple sclerosis patients☆

PubMed Central

Rahman, M. Tamizur; Sethi, Sean K.; Utriainen, David T.; Hewett, J. Joseph; Haacke, E. Mark

2014-01-01

Background and Purpose The use of magnetic resonance imaging (MRI) to assess the vascular nature of diseases such as multiple sclerosis (MS) is a growing field of research. This work reports on the application of MR angiographic (MRA) and venographic (MRV) techniques in assessing the extracranial vasculature in MS patients. Materials and Methods A standardized MRI protocol containing 2D TOF-MRV and dynamic 3D contrast-enhanced (CE) MRAV was run for 170 MS patients and 40 healthy controls (HC). The cross-sectional area (CSA) of the internal jugular veins (IJVs) was measured at three neck levels in all subjects for both MRV techniques to determine the presence of venous stenoses. All data were analyzed retrospectively. Results For the values where both methods showed signal, the 3D method showed larger CSA measurement values compared to 2D methods in both IJVs, in both MS and HC subjects which was confirmed with student paired t-tests. Of the 170 MS patients, 93 (55%) in CE-MRAV and 103 (61%) in TOF-MRV showed stenosis in at least one IJV. The corresponding numbers for the 40 HC subjects were 2 (5%) and 4 (10%), respectively. Carotid ectasias with IJV stenosis were seen in 26 cases (15%) with 3D CE-MRAV and were not observable with 2D TOF-MRV. Carotid ectasias were not seen in the HC group. In the 2D TOF-MRV data, banding of the IJVs related to slow flow was seen in 58 (34%) MS cases and in no HC cases. MS patients showed lower average CSAs than the HC subjects. Conclusion The 3D CE MRAV depicted the vascular anatomy more completely than the 2D TOF-MRV. However, the 3D CE MRAV does not provide any information about the flow characteristics which are indirectly available in the 2D TOF-MRV in those cases where there is slow flow. PMID:23850076

Obstacle Classification and 3D Measurement in Unstructured Environments Based on ToF Cameras

PubMed Central

Yu, Hongshan; Zhu, Jiang; Wang, Yaonan; Jia, Wenyan; Sun, Mingui; Tang, Yandong

2014-01-01

Inspired by the human 3D visual perception system, we present an obstacle detection and classification method based on the use of Time-of-Flight (ToF) cameras for robotic navigation in unstructured environments. The ToF camera provides 3D sensing by capturing an image along with per-pixel 3D space information. Based on this valuable feature and human knowledge of navigation, the proposed method first removes irrelevant regions which do not affect robot's movement from the scene. In the second step, regions of interest are detected and clustered as possible obstacles using both 3D information and intensity image obtained by the ToF camera. Consequently, a multiple relevance vector machine (RVM) classifier is designed to classify obstacles into four possible classes based on the terrain traversability and geometrical features of the obstacles. Finally, experimental results in various unstructured environments are presented to verify the robustness and performance of the proposed approach. We have found that, compared with the existing obstacle recognition methods, the new approach is more accurate and efficient. PMID:24945679

Visual control of robots using range images.

PubMed

Pomares, Jorge; Gil, Pablo; Torres, Fernando

2010-01-01

In the last years, 3D-vision systems based on the time-of-flight (ToF) principle have gained more importance in order to obtain 3D information from the workspace. In this paper, an analysis of the use of 3D ToF cameras to guide a robot arm is performed. To do so, an adaptive method to simultaneous visual servo control and camera calibration is presented. Using this method a robot arm is guided by using range information obtained from a ToF camera. Furthermore, the self-calibration method obtains the adequate integration time to be used by the range camera in order to precisely determine the depth information.

Neurovascular Study of the Trigeminal Nerve at 3 T MRI

PubMed Central

Gonzalez, Nadia; Muñoz, Alexandra; Bravo, Fernando; Sarroca, Daniel; Morales, Carlos

2015-01-01

This study aimed to show a novel visualization method to investigate neurovascular compression of the trigeminal nerve (TN) using a volume-rendering fusion imaging technique of 3D fast imaging employing steady-state acquisition (3D FIESTA) and coregistered 3D time of flight MR angiography (3D TOF MRA) sequences, which we called “neurovascular study of the trigeminal nerve”. We prospectively studied 30 patients with unilateral trigeminal neuralgia (TN) and 50 subjects without symptoms of TN (control group), on a 3 Tesla scanner. All patients were assessed using 3D FIESTA and 3D TOF MRA sequences centered on the pons, as well as a standard brain protocol including axial T1, T2, FLAIR and GRE sequences to exclude other pathologies that could cause TN. Post-contrast T1-weighted sequences were also performed. All cases showing arterial imprinting on the trigeminal nerve (n = 11) were identified on the ipsilateral side of the pain. No significant relationship was found between the presence of an artery in contact with the trigeminal nerve and TN. Eight cases were found showing arterial contact on the ipsilateral side of the pain and five cases of arterial contact on the contralateral side. The fusion imaging technique of 3D FIESTA and 3D TOF MRA sequences, combining the high anatomical detail provided by the 3D FIESTA sequence with the 3D TOF MRA sequence and its capacity to depict arterial structures, results in a tool that enables quick and efficient visualization and assessment of the relationship between the trigeminal nerve and the neighboring vascular structures. PMID:25924169

Role of MRA in the detection of intracranial aneurysm in the acute phase of subarachnoid hemorrhage.

PubMed

Pierot, Laurent; Portefaix, Christophe; Rodriguez-Régent, Christine; Gallas, Sophie; Meder, Jean-François; Oppenheim, Catherine

2013-07-01

Magnetic resonance angiography (MRA) has been evaluated for the detection of unruptured intracranial aneurysms with favorable results at 3 Tesla (3T) and with similar diagnostic accuracy as both 3D time-of-flight (3D-TOF) and contrast-enhanced (CE-MRA) MRA. However, the diagnostic value and place of MRA in the detection of ruptured aneurysms has been little evaluated. Thus, the goal of this prospective single-center series was to assess the feasibility and diagnostic value of 3T 3D-TOF MRA and CE-MRA for aneurysm detection in acute non-traumatic subarachnoid hemorrhage (SAH). From March 2006 to December 2007, all consecutive patients admitted to our hospital with acute non-traumatic SAH (≤10 days) were prospectively included in this study evaluating MRA in the diagnostic workup of SAH. Feasibility of MRA and sensitivity/specificity of 3D-TOF and CE-MRA were assessed compared with gold standard DSA. In all, 84 consecutive patients (45 women, 39 men; age 23-86 years) were included. The feasibility of MRA was low (43/84, 51.2%). The reasons given for patients not undergoing magnetic resonance imaging (MRI) examination were clinical status (27 patients), potential delay in aneurysm treatment (11 patients) and contraindications to MRI (three patients). In patients explored by MRA, the sensitivity of CE-MRA (95%) was higher compared with 3D-TOF (86%) with similar specificity (80%). Also, 3D-TOF missed five aneurysms while CE-MRA missed two. The value of MRA in the diagnostic workup of ruptured aneurysms is limited due to its low feasibility during the acute phase of bleeding. Sensitivity for aneurysm detection was good for both MRA techniques, but tended to be better with CE-MRA. Copyright © 2013. Published by Elsevier Masson SAS.

A novel particle time of flight diagnostic for measurements of shock- and compression-bang times in D3He and DT implosions at the NIF.

PubMed

Rinderknecht, H G; Johnson, M Gatu; Zylstra, A B; Sinenian, N; Rosenberg, M J; Frenje, J A; Waugh, C J; Li, C K; Sèguin, F H; Petrasso, R D; Rygg, J R; Kimbrough, J R; MacPhee, A; Collins, G W; Hicks, D; Mackinnon, A; Bell, P; Bionta, R; Clancy, T; Zacharias, R; Döppner, T; Park, H S; LePape, S; Landen, O; Meezan, N; Moses, E I; Glebov, V U; Stoeckl, C; Sangster, T C; Olson, R; Kline, J; Kilkenny, J

2012-10-01

The particle-time-of-flight (pTOF) diagnostic, fielded alongside a wedge range-filter (WRF) proton spectrometer, will provide an absolute timing for the shock-burn weighted ρR measurements that will validate the modeling of implosion dynamics at the National Ignition Facility (NIF). In the first phase of the project, pTOF has recorded accurate bang times in cryogenic DT, DT exploding pusher, and D(3)He implosions using DD or DT neutrons with an accuracy better than ±70 ps. In the second phase of the project, a deflecting magnet will be incorporated into the pTOF design for simultaneous measurements of shock- and compression-bang times in D(3)He-filled surrogate implosions using D(3)He protons and DD-neutrons, respectively.

The applied research of MRI with ASSET-EPI-FLAIR combined with 3D TOF MRA sequences in the assessment of patients with acute cerebral infarction.

PubMed

Lin, Zhichao; Guo, Zexiong; Qiu, Lin; Yang, Wanyoug; Lin, Mingxia

2016-12-01

Background To extend the time window for thrombolysis, reducing the time for diagnosis and detection of acute cerebral infarction seems to be warranted. Purpose To evaluate the feasibility of implementing an array spatial sensitivity technique (ASSET)-echo-planar imaging (EPI)-fluid attenuated inversion recovery (FLAIR) (AE-FLAIR) sequence into an acute cerebral infarction magnetic resonance (MR) evaluation protocol, and to assess the diagnostic value of AE-FLAIR combined with three-dimensional time-of-flight MR angiography (3D TOF MRA). Material and Methods A total of 100 patients (68 men, 32 women; age range, 44-82 years) with acute cerebral infarction, including 50 consecutive uncooperative and 50 cooperative patients, were evaluated with T1-weighted (T1W) imaging, T2-weighted (T2W) imaging, FLAIR, diffusion-weighted imaging (DWI), 3D TOF, EPI-FLAIR, and AE-FLAIR. Conventional FLAIR, EPI-FLAIR, and AE-FLAIR were assessed by two observers independently for image quality. The optimized group (AE-FLAIR and 3D TOF) and the control group (T1W imaging, T2W imaging, conventional FLAIR, DWI, and 3D TOF) were compared for evaluation time and diagnostic accuracy. Results One hundred and twenty-five lesions were detected and images having adequate diagnostic image quality were in 73% of conventional FLAIR, 62% of EPI-FLAIR, and 89% of AE-FLAIR. The detection time was 12 ± 1 min with 76% accuracy and 4 ± 0.5 min with 100% accuracy in the control and the optimized groups, respectively. Inter-observer agreements of κ = 0.78 and κ = 0.81 were for the optimized group and control group, respectively. Conclusion With reduced acquisition time and better image quality, AE-FLAIR combined with 3D TOF may be used as a rapid diagnosis tool in patients with acute cerebral infarction, especially in uncooperative patients.

Dose Optimization in TOF-PET/MR Compared to TOF-PET/CT

PubMed Central

Queiroz, Marcelo A.; Delso, Gaspar; Wollenweber, Scott; Deller, Timothy; Zeimpekis, Konstantinos; Huellner, Martin; de Galiza Barbosa, Felipe; von Schulthess, Gustav; Veit-Haibach, Patrick

2015-01-01

Purpose To evaluate the possible activity reduction in FDG-imaging in a Time-of-Flight (TOF) PET/MR, based on cross-evaluation of patient-based NECR (noise equivalent count rate) measurements in PET/CT, cross referencing with phantom-based NECR curves as well as initial evaluation of TOF-PET/MR with reduced activity. Materials and Methods A total of 75 consecutive patients were evaluated in this study. PET/CT imaging was performed on a PET/CT (time-of-flight (TOF) Discovery D 690 PET/CT). Initial PET/MR imaging was performed on a newly available simultaneous TOF-PET/MR (Signa PET/MR). An optimal NECR for diagnostic purposes was defined in clinical patients (NECRP) in PET/CT. Subsequent optimal activity concentration at the acquisition time ([A]0) and target NECR (NECRT) were obtained. These data were used to predict the theoretical FDG activity requirement of the new TOF-PET/MR system. Twenty-five initial patients were acquired with (retrospectively reconstructed) different imaging times equivalent for different activities on the simultaneous PET/MR for the evaluation of clinically realistic FDG-activities. Results The obtained values for NECRP, [A]0 and NECRT were 114.6 (± 14.2) kcps (Kilocounts per second), 4.0 (± 0.7) kBq/mL and 45 kcps, respectively. Evaluating the NECRT together with the phantom curve of the TOF-PET/MR device, the theoretical optimal activity concentration was found to be approximately 1.3 kBq/mL, which represents 35% of the activity concentration required by the TOF-PET/CT. Initial evaluation on patients in the simultaneous TOF-PET/MR shows clinically realistic activities of 1.8 kBq/mL, which represent 44% of the required activity. Conclusion The new TOF-PET/MR device requires significantly less activity to generate PET-images with good-to-excellent image quality, due to improvements in detector geometry and detector technologies. The theoretically achievable dose reduction accounts for up to 65% but cannot be fully translated into clinical routine based on the coils within the FOV and MR-sequences applied at the same time. The clinically realistic reduction in activity is slightly more than 50%. Further studies in a larger number of patients are needed to confirm our findings. PMID:26147919

Validity of computational hemodynamics in human arteries based on 3D time-of-flight MR angiography and 2D electrocardiogram gated phase contrast images

NASA Astrophysics Data System (ADS)

Yu, Huidan (Whitney); Chen, Xi; Chen, Rou; Wang, Zhiqiang; Lin, Chen; Kralik, Stephen; Zhao, Ye

2015-11-01

In this work, we demonstrate the validity of 4-D patient-specific computational hemodynamics (PSCH) based on 3-D time-of-flight (TOF) MR angiography (MRA) and 2-D electrocardiogram (ECG) gated phase contrast (PC) images. The mesoscale lattice Boltzmann method (LBM) is employed to segment morphological arterial geometry from TOF MRA, to extract velocity profiles from ECG PC images, and to simulate fluid dynamics on a unified GPU accelerated computational platform. Two healthy volunteers are recruited to participate in the study. For each volunteer, a 3-D high resolution TOF MRA image and 10 2-D ECG gated PC images are acquired to provide the morphological geometry and the time-varying flow velocity profiles for necessary inputs of the PSCH. Validation results will be presented through comparisons of LBM vs. 4D Flow Software for flow rates and LBM simulation vs. MRA measurement for blood flow velocity maps. Indiana University Health (IUH) Values Fund.

The influence of different signal-to-background ratios on spatial resolution and F18-FDG-PET quantification using point spread function and time-of-flight reconstruction.

PubMed

Rogasch, Julian Mm; Hofheinz, Frank; Lougovski, Alexandr; Furth, Christian; Ruf, Juri; Großer, Oliver S; Mohnike, Konrad; Hass, Peter; Walke, Mathias; Amthauer, Holger; Steffen, Ingo G

2014-12-01

F18-fluorodeoxyglucose positron-emission tomography (FDG-PET) reconstruction algorithms can have substantial influence on quantitative image data used, e.g., for therapy planning or monitoring in oncology. We analyzed radial activity concentration profiles of differently reconstructed FDG-PET images to determine the influence of varying signal-to-background ratios (SBRs) on the respective spatial resolution, activity concentration distribution, and quantification (standardized uptake value [SUV], metabolic tumor volume [MTV]). Measurements were performed on a Siemens Biograph mCT 64 using a cylindrical phantom containing four spheres (diameter, 30 to 70 mm) filled with F18-FDG applying three SBRs (SBR1, 16:1; SBR2, 6:1; SBR3, 2:1). Images were reconstructed employing six algorithms (filtered backprojection [FBP], FBP + time-of-flight analysis [FBP + TOF], 3D-ordered subset expectation maximization [3D-OSEM], 3D-OSEM + TOF, point spread function [PSF], PSF + TOF). Spatial resolution was determined by fitting the convolution of the object geometry with a Gaussian point spread function to radial activity concentration profiles. MTV delineation was performed using fixed thresholds and semiautomatic background-adapted thresholding (ROVER, ABX, Radeberg, Germany). The pairwise Wilcoxon test revealed significantly higher spatial resolutions for PSF + TOF (up to 4.0 mm) compared to PSF, FBP, FBP + TOF, 3D-OSEM, and 3D-OSEM + TOF at all SBRs (each P < 0.05) with the highest differences for SBR1 decreasing to the lowest for SBR3. Edge elevations in radial activity profiles (Gibbs artifacts) were highest for PSF and PSF + TOF declining with decreasing SBR (PSF + TOF largest sphere; SBR1, 6.3%; SBR3, 2.7%). These artifacts induce substantial SUVmax overestimation compared to the reference SUV for PSF algorithms at SBR1 and SBR2 leading to substantial MTV underestimation in threshold-based segmentation. In contrast, both PSF algorithms provided the lowest deviation of SUVmean from reference SUV at SBR1 and SBR2. At high contrast, the PSF algorithms provided the highest spatial resolution and lowest SUVmean deviation from the reference SUV. In contrast, both algorithms showed the highest deviations in SUVmax and threshold-based MTV definition. At low contrast, all investigated reconstruction algorithms performed approximately equally. The use of PSF algorithms for quantitative PET data, e.g., for target volume definition or in serial PET studies, should be performed with caution - especially if comparing SUV of lesions with high and low contrasts.

Optimal MRI sequence for identifying occlusion location in acute stroke: which value of time-resolved contrast-enhanced MRA?

PubMed

Le Bras, A; Raoult, H; Ferré, J-C; Ronzière, T; Gauvrit, J-Y

2015-06-01

Identifying occlusion location is crucial for determining the optimal therapeutic strategy during the acute phase of ischemic stroke. The purpose of this study was to assess the diagnostic efficacy of MR imaging, including conventional sequences plus time-resolved contrast-enhanced MRA in comparison with DSA for identifying arterial occlusion location. Thirty-two patients with 34 occlusion levels referred for thrombectomy during acute cerebral stroke events were consecutively included from August 2010 to December 2012. Before thrombectomy, we performed 3T MR imaging, including conventional 3D-TOF and gradient-echo T2 sequences, along with time-resolved contrast-enhanced MRA of the extra- and intracranial arteries. The 3D-TOF, gradient-echo T2, and time-resolved contrast-enhanced MRA results were consensually assessed by 2 neuroradiologists and compared with prethrombectomy DSA results in terms of occlusion location. The Wilcoxon test was used for statistical analysis to compare MR imaging sequences with DSA, and the κ coefficient was used to determine intermodality agreement. The occlusion level on the 3D-TOF and gradient-echo T2 images differed significantly from that of DSA (P < .001 and P = .002, respectively), while no significant difference was observed between DSA and time-resolved contrast-enhanced MRA (P = .125). κ coefficients for intermodality agreement with DSA (95% CI, percentage agreement) were 0.43 (0.3%-0.6; 62%), 0.32 (0.2%-0.5; 56%), and 0.81 (0.6%-1.0; 88%) for 3D-TOF, gradient-echo T2, and time-resolved contrast-enhanced MRA, respectively. The time-resolved contrast-enhanced MRA sequence proved reliable for identifying occlusion location in acute stroke with performance superior to that of 3D-TOF and gradient-echo T2 sequences. © 2015 by American Journal of Neuroradiology.

Abnormal biventricular performance in asymptomatic adolescents late after repaired Tetralogy of Fallot: Combined two-dimensional speckle tracking and three-dimensional echocardiography study.

PubMed

Weng, Ken-Pen; Hung, Yu-Chi; Huang, Shih-Hui; Wu, Huang-Wei; Chien, Kuang-Jen; Lin, Chu-Chuan; Peng, Hsu-Hsia; Wu, Ming-Ting

2018-02-01

The aim of this prospective study was to assess biventricular performance in asymptomatic adolescents with repaired tetralogy of Fallot (TOF) using 2D speckle tracking and real time 3D echocardiography simultaneously. We studied 31 patients with repaired TOF (M/F: 22/9, age: 16.1 ± 6.1 yrs) who had history of cardiac surgery with mean follow-up duration of 12.8 years, and 32 age- and sex-matched normal individuals (M/F: 23/9, age: 16.6 ± 5.1 yrs). All subjects underwent speckle tracking and 3D echocardiography, electrocardiogram, treadmill, and blood sampling for measurement of brain natriuretic peptide (BNP). Compared to the control group, the TOF group had higher BNP level (31.8 ± 21.4 vs 14.1 ± 12.4 pg/ml, p < 0.01), lower peak oxygen consumption (8.4 ± 1.7 vs 9.9 ± 1.6 ml/kg/min, p < 0.05), and longer QRS duration (126 ± 30 vs 82 ± 9 ms, p < 0.01). Patients with repaired TOF had significantly impaired right ventricle (RV) global and all six regional longitudinal strain and strain rate than normal controls. Left ventricle (LV) global and mainly apical regional longitudinal strain and strain rate were reduced in patients with repaired TOF. There was a significant correlation of global longitudinal strain (r = 0.456, p = 0.01) and global time to peak longitudinal strain (r = 0.484, p < 0.01) between LV and RV in patients with repaired TOF. In terms of 3D echo cardiographic volume data, patients with repaired TOF had lower LV stroke volume index (p < 0.05), but higher RV end diastolic volume index (p < 0.01), RV end systolic volume index (p < 0.01), RV stroke volume index (p < 0.01), and pulmonary regurgitation fraction (p < 0.01) than normal controls. Our results suggest asymptomatic adolescents with repaired TOF had abnormal biventricular myocardial performance, as demonstrated by combined 2D speckle-tracking and 3D echocardiography. The implications of these findings for management of adolescents late after repaired TOF remain to be determined. Copyright © 2017. Published by Elsevier Taiwan LLC.

Sensitivity estimation in time-of-flight list-mode positron emission tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herraiz, J. L.; Sitek, A., E-mail: sarkadiu@gmail.com

Purpose: An accurate quantification of the images in positron emission tomography (PET) requires knowing the actual sensitivity at each voxel, which represents the probability that a positron emitted in that voxel is finally detected as a coincidence of two gamma rays in a pair of detectors in the PET scanner. This sensitivity depends on the characteristics of the acquisition, as it is affected by the attenuation of the annihilation gamma rays in the body, and possible variations of the sensitivity of the scanner detectors. In this work, the authors propose a new approach to handle time-of-flight (TOF) list-mode PET data,more » which allows performing either or both, a self-attenuation correction, and self-normalization correction based on emission data only. Methods: The authors derive the theory using a fully Bayesian statistical model of complete data. The authors perform an initial evaluation of algorithms derived from that theory and proposed in this work using numerical 2D list-mode simulations with different TOF resolutions and total number of detected coincidences. Effects of randoms and scatter are not simulated. Results: The authors found that proposed algorithms successfully correct for unknown attenuation and scanner normalization for simulated 2D list-mode TOF-PET data. Conclusions: A new method is presented that can be used for corrections for attenuation and normalization (sensitivity) using TOF list-mode data.« less

Sensitivity estimation in time-of-flight list-mode positron emission tomography.

PubMed

Herraiz, J L; Sitek, A

2015-11-01

An accurate quantification of the images in positron emission tomography (PET) requires knowing the actual sensitivity at each voxel, which represents the probability that a positron emitted in that voxel is finally detected as a coincidence of two gamma rays in a pair of detectors in the PET scanner. This sensitivity depends on the characteristics of the acquisition, as it is affected by the attenuation of the annihilation gamma rays in the body, and possible variations of the sensitivity of the scanner detectors. In this work, the authors propose a new approach to handle time-of-flight (TOF) list-mode PET data, which allows performing either or both, a self-attenuation correction, and self-normalization correction based on emission data only. The authors derive the theory using a fully Bayesian statistical model of complete data. The authors perform an initial evaluation of algorithms derived from that theory and proposed in this work using numerical 2D list-mode simulations with different TOF resolutions and total number of detected coincidences. Effects of randoms and scatter are not simulated. The authors found that proposed algorithms successfully correct for unknown attenuation and scanner normalization for simulated 2D list-mode TOF-PET data. A new method is presented that can be used for corrections for attenuation and normalization (sensitivity) using TOF list-mode data.

Validation of a highly integrated SiPM readout system with a TOF-PET demonstrator

NASA Astrophysics Data System (ADS)

Niknejad, T.; Setayeshi, S.; Tavernier, S.; Bugalho, R.; Ferramacho, L.; Di Francesco, A.; Leong, C.; Rolo, M. D.; Shamshirsaz, M.; Silva, J. C.; Silva, R.; Silveira, M.; Zorraquino, C.; Varela, J.

2016-12-01

We have developed a highly integrated, fast and compact readout electronics for Silicon Photomultiplier (SiPM) based Time of Flight Positron Emission Tomography (TOF-PET) scanners. The readout is based on the use of TOP-PET Application Specific Integrated Circuit (PETsys TOFPET1 ASIC) with 64 channels, each with its amplifier, discriminator, Time to Digital Converter (TDC) and amplitude determination using Time Over Threshold (TOT). The ASIC has 25 ps r.m.s. intrinsic time resolution and fully digital output. The system is optimised for high rates, good timing, low power consumption and low cost. For validating the readout electronics, we have built a technical PET scanner, hereafter called ``demonstrator'', with 2'048 SiPM channels. The PET demonstrator has 16 compact Detector Modules (DM). Each DM has two ASICs reading 128 SiPM pixels in one-to-one coupling to 128 Lutetium Yttrium Orthosilicate (LYSO) crystals measuring 3.1 × 3.1 × 15 mm3 each. The data acquisition system for the demonstrator has two Front End Boards type D (FEB/D), each collecting the data of 1'024 channels (8 DMs), and transmitting assembled data frames through a serial link (4.8 Gbps), to a single Data Acquisition (DAQ) board plugged into the Peripheral Component Interconnect Express (PCIe) bus of the data acquisition PC. Results obtained with this PET demonstrator are presented.

Clinical application of three-dimensional reconstruction and rapid prototyping technology of multislice spiral computed tomography angiography for the repair of ventricular septal defect of tetralogy of Fallot.

PubMed

Ma, X J; Tao, L; Chen, X; Li, W; Peng, Z Y; Chen, Y; Jin, J; Zhang, X L; Xiong, Q F; Zhong, Z L; Chen, X F

2015-02-13

Three-dimensional (3D) reconstruction and rapid prototyping technology (RPT) of multislice spiral computed tomography angiography (CTA) was applied to prepare physical models of the heart and ventricular septal defects of tetralogy of Fallot (ToF) patients in order to explore their applications in the diagnosis and treatment of this complex heart disease. CTA data of 35 ToF patients were collected to prepare l:l 3D solid models using digital 3D reconstruction and RPT, and the resultant models were used intraoperatively as reference. The operations of all 35 patients were completed under the guidance of the 3D solid model, without difficulty. Intraoperative findings of the patients were consistent with the morphological and size changes of the 3D solid model, and no significant differences were found between the patches obtained from the 3D solid model and the actual intraoperative measurements (t = 0.83, P = 0.412). 3D reconstruction and RPT of multislice spiral CTA can accurately and intuitively reflect the anatomy of ventricular septal defects in ToF patients, providing the foundation for a solid model of the complex congenital heart.

Image quality improvement in three-dimensional time-of-flight magnetic resonance angiography using the subtraction method for brain and temporal bone diseases.

PubMed

Peng, Shu-Hui; Shen, Chao-Yu; Wu, Ming-Chi; Lin, Yue-Der; Huang, Chun-Huang; Kang, Ruei-Jin; Tyan, Yeu-Sheng; Tsao, Teng-Fu

2013-08-01

Time-of-flight (TOF) magnetic resonance (MR) angiography is based on flow-related enhancement using the T1-weighted spoiled gradient echo, or the fast low-angle shot gradient echo sequence. However, materials with short T1 relaxation times may show hyperintensity signals and contaminate the TOF images. The objective of our study was to determine whether subtraction three-dimensional (3D) TOF MR angiography improves image quality in brain and temporal bone diseases with unwanted contaminations with short T1 relaxation times. During the 12-month study period, patients who had masses with short T1 relaxation times noted on precontrast T1-weighted brain MR images and 24 healthy volunteers were scanned using conventional and subtraction 3D TOF MR angiography. The qualitative evaluation of each MR angiogram was based on signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and scores in three categories, namely, (1) presence of misregistration artifacts, (2) ability to display arterial anatomy selectively (without contamination by materials with short T1 relaxation times), and (3) arterial flow-related enhancement. We included 12 patients with intracranial hematomas, brain tumors, or middle-ear cholesterol granulomas. Subtraction 3D TOF MR angiography yielded higher CNRs between the area of the basilar artery (BA) and normal-appearing parenchyma of the brain and lower SNRs in the area of the BA compared with the conventional technique (147.7 ± 77.6 vs. 130.6 ± 54.2, p < 0.003 and 162.5 ± 79.9 vs. 194.3 ± 62.3, p < 0.001, respectively) in all 36 cases. The 3D subtraction angiography did not deteriorate image quality with misregistration artifacts and showed a better selective display of arteries (p < 0.0001) and arterial flow-related enhancement (p < 0.044) than the conventional method. Subtraction 3D TOF MR angiography is more appropriate than the conventional method in improving the image quality in brain and temporal bone diseases with unwanted contaminations with short T1 relaxation times. Copyright © 2013. Published by Elsevier B.V.

Investigation of practical initial attenuation image estimates in TOF-MLAA reconstruction for PET/MR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Ju-Chieh, E-mail: chengjuchieh@gmail.com; Y

Purpose: Time-of-flight joint attenuation and activity positron emission tomography reconstruction requires additional calibration (scale factors) or constraints during or post-reconstruction to produce a quantitative μ-map. In this work, the impact of various initializations of the joint reconstruction was investigated, and the initial average mu-value (IAM) method was introduced such that the forward-projection of the initial μ-map is already very close to that of the reference μ-map, thus reducing/minimizing the offset (scale factor) during the early iterations of the joint reconstruction. Consequently, the accuracy and efficiency of unconstrained joint reconstruction such as time-of-flight maximum likelihood estimation of attenuation and activity (TOF-MLAA)more » can be improved by the proposed IAM method. Methods: 2D simulations of brain and chest were used to evaluate TOF-MLAA with various initial estimates which include the object filled with water uniformly (conventional initial estimate), bone uniformly, the average μ-value uniformly (IAM magnitude initialization method), and the perfect spatial μ-distribution but with a wrong magnitude (initialization in terms of distribution). 3D GATE simulation was also performed for the chest phantom under a typical clinical scanning condition, and the simulated data were reconstructed with a fully corrected list-mode TOF-MLAA algorithm with various initial estimates. The accuracy of the average μ-values within the brain, chest, and abdomen regions obtained from the MR derived μ-maps was also evaluated using computed tomography μ-maps as the gold-standard. Results: The estimated μ-map with the initialization in terms of magnitude (i.e., average μ-value) was observed to reach the reference more quickly and naturally as compared to all other cases. Both 2D and 3D GATE simulations produced similar results, and it was observed that the proposed IAM approach can produce quantitative μ-map/emission when the corrections for physical effects such as scatter and randoms were included. The average μ-value obtained from MR derived μ-map was accurate within 5% with corrections for bone, fat, and uniform lungs. Conclusions: The proposed IAM-TOF-MLAA can produce quantitative μ-map without any calibration provided that there are sufficient counts in the measured data. For low count data, noise reduction and additional regularization/rescaling techniques need to be applied and investigated. The average μ-value within the object is prior information which can be extracted from MR and patient database, and it is feasible to obtain accurate average μ-value using MR derived μ-map with corrections as demonstrated in this work.« less

Comparison of TOF MRA, Contrast-Enhanced MRA and Subtracted CTA from CTP in Residue Evaluation of Treated Intracranial Aneurysms.

PubMed

Dündar, Tolga Turan; Aralaşmak, Ayşe; Özdemir, Hüseyin; Seyithanoğlu, Mehmet Hakan; Uysal, Ömer; Toprak, Hüseyin; Kitiş, Serkan; Özek, Erdinç; Alkan, Alpay

2017-10-18

To compare effectiveness of contrast-enhanced MRA (CE-MRA), 3D-Time-of-flight MRA (3D-TOF-MRA) and subtracted CTA from CTP (sub-CTA) in residue evaluation of intracranial aneurysms treated either with coiling or clipping. Sixteen treated aneurysms, which were evaluated with three methods within two weeks after the operation, were enrolled. The success of each imaging techniques in demonstration of residue aneurysm and nearby vessels was compared by Fisher\\'s Exact Test. The differences among three was evaluated by Cochran\\'s Q test (p ≤ 0.05). Perfusion abnormality was noted in % 81 of clipped and none of coiled patients. Vessel visualization in the vicinity of aneurysm was better in sub-CTA, followed by CE-MRA. In clipped aneurysms, sub-CTA revealed residue aneurysms in % 16,7 of the patients while 3D-TOF-MRA and CE-MRA revealed none. In coiled aneurysms, CE-MRA revealed residue aneurysms in 100 %, and TOF-MRA in 33,3 % while sub-CTA revealed none. Although dramatic differences were noted in the evaluation of residue aneurysm as well as nearby vessel visualization, no statistical significance noted due to very few patients in subcategories Conclusion: This is first study comparing the effectiveness of CE-MRA, 3D-TOF MRA and sub-CTA in residue aneurysms evaluation. Vessel visualization in the vicinity of aneurysm was better in sub-CTA in all regardless of coiling or clipping. Residue aneurysms were more commonly revealed by CE-MRA in coiled patients and more commonly and better shown by sub-CTA in clipped patients in addition of showing perfusion abnormality that's is more common in clipped patients.

Evaluation of the applicability of territorial arterial spin labeling in meningiomas for presurgical assessments compared with 3-dimensional time-of-flight magnetic resonance angiography.

PubMed

Lu, Yiping; Luan, Shihai; Liu, Li; Xiong, Ji; Wen, Jianbo; Qu, Jianxun; Geng, Daoying; Yin, Bo

2017-10-01

To prospectively evaluate the application of territorial arterial spin labelling (t-ASL) in comparison with unenhanced three-dimensional time-of-flight magnetic resonance angiography (3D-TOF-MRA) in the identification of the feeding vasculature of meningiomas. Thirty consecutive patients with suspected meningiomas underwent conventional MR imaging, unenhanced 3D-TOF-MRA and t-ASL scanning. Four experienced neuro-radiologists assessed the feeding vessels with different techniques separately. For the identification of the origin of the feeding arteries on t-ASL, the inter-observer agreement was excellent (к = 0.913), while the inter-observer agreement of 3D-TOF-MRA was good (к = 0.653). The inter-modality agreement between t-ASL and 3D-TOF-MRA for the feeding arteries was moderate (к = 0.514). All 8 patients with motor or sensory disorders proved to have meningiomas supplied completely or partially by the internal carotid arteries, while all 14 patients with meningiomas supplied by the external carotid arteries or basilar arteries didn't show any symptoms concerning motor or sensory disorders (p = 0.003). T-ASL could complement unenhanced 3D-TOF-MRA and increase accuracy in the identification of the supplying arteries of meningiomas in a safe, intuitive, non-radioactive manner. The information about feeding arteries was potentially related to patients' symptoms and pathology, making it more crucial for neurosurgeons in planning surgery as well as evaluating prognosis. • A comprehensive understanding of feeding vasculature is helpful for optimized treatment decisions. • T-ASL could identify main supplying arteries of meningiomas with excellent inter-observer agreement. • The inter-modality agreement for identification of the main feeding arteries was moderate. • Blood supply from ICAs was related to motor or sensory disorders. • High-level meningiomas were found to have double main supplying arteries.

Semi Quantitative MALDI TOF for Antimicrobial Susceptibility Testing in Staphylococcus aureus

DTIC Science & Technology

2017-08-31

Semi- quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus 1 aureus 2 3 4 Tucker Maxson,a Cheryl L. Taylor-Howell,a...Timothy D. Minoguea# 5 6 Diagnostic Systems Division, United States Army Medical Research Institute of Infectious 7 Disease, Fort Detrick, MD...USAa 8 9 Running Title: Quantitative MALDI for AST in S. aureus 10 #Address correspondence to Timothy D. Minogue, timothy.d.minogue.civ@mail.mil

High-dynamic-range neutron time-of-flight detector used to infer the D(t,n){sup 4}He and D(d,n){sup 3}He reaction yield and ion temperature on OMEGA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forrest, C. J., E-mail: cforrest@lle.rochester.edu; Glebov, V. Yu.; Goncharov, V. N.

Upgraded microchannel-plate–based photomultiplier tubes (MCP-PMT’s) with increased stability to signal-shape linearity have been implemented on the 13.4-m neutron time-of-flight (nTOF) detector at the Omega Laser Facility. This diagnostic uses oxygenated xylene doped with diphenyloxazole C{sub 15}H{sub 11}NO + p-bis-(o-methylstyryl)-benzene (PPO + bis-MSB) wavelength shifting dyes and is coupled through four viewing ports to fast-gating MCP-PMT’s, each with a different gain to allow one to measure the light output over a dynamic range of 1 × 10{sup 6}. With these enhancements, the 13.4-m nTOF can measure the D(t,n){sup 4}He and D(d,n){sup 3}He reaction yields and average ion temperatures in a singlemore » line of sight. Once calibrated for absolute neutron sensitivity, the nTOF detectors can be used to measure the neutron yield from 1 × 10{sup 9} to 1 × 10{sup 14} and the ion temperature with an accuracy approaching 5% for both the D(t,n){sup 4}He and D(d,n){sup 3}He reactions.« less

High-resolution, time-resolved MRA provides superior definition of lower-extremity arterial segments compared to 2D time-of-flight imaging.

PubMed

Thornton, F J; Du, J; Suleiman, S A; Dieter, R; Tefera, G; Pillai, K R; Korosec, F R; Mistretta, C A; Grist, T M

2006-08-01

To evaluate a novel time-resolved contrast-enhanced (CE) projection reconstruction (PR) magnetic resonance angiography (MRA) method for identifying potential bypass graft target vessels in patients with Class II-IV peripheral vascular disease. Twenty patients (M:F = 15:5, mean age = 58 years, range = 48-83 years), were recruited from routine MRA referrals. All imaging was performed on a 1.5 T MRI system with fast gradients (Signa LX; GE Healthcare, Waukesha, WI). Images were acquired with a novel technique that combined undersampled PR with a time-resolved acquisition to yield an MRA method with high temporal and spatial resolution. The method is called PR hyper time-resolved imaging of contrast kinetics (PR-hyperTRICKS). Quantitative and qualitative analyses were used to compare two-dimensional (2D) time-of-flight (TOF) and PR-hyperTRICKS in 13 arterial segments per lower extremity. Statistical analysis was performed with the Wilcoxon signed-rank test. Fifteen percent (77/517) of the vessels were scored as missing or nondiagnostic with 2D TOF, but were scored as diagnostic with PR-hyperTRICKS. Image quality was superior with PR-hyperTRICKS vs. 2D TOF (on a four-point scale, mean rank = 3.3 +/- 1.2 vs. 2.9 +/- 1.2, P < 0.0001). PR-hyperTRICKS produced images with high contrast-to-noise ratios (CNR) and high spatial and temporal resolution. 2D TOF images were of inferior quality due to moderate spatial resolution, inferior CNR, greater flow-related artifacts, and absence of temporal resolution. PR-hyperTRICKS provides superior preoperative assessment of lower limb ischemia compared to 2D TOF.

Neurovascular stent artifacts in 3D-TOF and 3D-PCMRI: Influence of stent design on flow measurement.

PubMed

Bouillot, Pierre; Brina, Olivier; Delattre, Bénédicte M A; Ouared, Rafik; Pellaton, Alain; Yilmaz, Hasan; Machi, Paolo; Lovblad, Karl-Olof; Farhat, Mohamed; Pereira, Vitor Mendes; Vargas, Maria Isabel

2018-06-12

The morphological and hemodynamic evaluations of neurovascular diseases treated with stents would benefit from noninvasive imaging techniques such as 3D time-of-flight MRI (3D-TOF) and 3D phase contrast MRI (3D-PCMRI). For this purpose, a comprehensive evaluation of the stent artifacts and their impact on the flow measurement is critical. The artifacts of a representative sample of neurovascular stents were evaluated in vitro with 3D-TOF and 3D-PCMRI sequences. The dependency of the artifacts with respect to the orientation was analyzed for each stent design as well as the impact on the flow measurement accuracy. Furthermore, the 3D-PCMRI data of four patients carrying intracranial aneurysms treated with flow diverter stents were analyzed as illustrative examples. The stent artifacts were mainly confined to the stent lumen therefore indicating the leading role of shielding effect. The influence of the stent design and its orientation with respect to the transmitting MR coils were highlighted. The artifacts impacted the 3D-PCMRI velocities mainly in the low magnitude domains, which were discarded from the analysis ensuring reliable near-stent velocities. The feasibility of in-stent flow measurements was confirmed in vivo on two patients who showed strong correlation between flow and geometric features. In two other patients, the consistency of out-of-stent velocities was verified qualitatively through intra-aneurysmal streamlines except when susceptibility artifacts occurred. The present results motivate the conception of low inductance or nonconductive stent design. Furthermore, the feasibility of near-stent 3D-PCMRI measurements opens the door to clinical applications like the post-treatment follow-up of stenoses or intracranial aneurysms. © 2018 International Society for Magnetic Resonance in Medicine.

Preoperative evaluation of venous systems with 3-dimensional contrast-enhanced magnetic resonance venography in brain tumors: comparison with time-of-flight magnetic resonance venography and digital subtraction angiography.

PubMed

Lee, Jong-Myung; Jung, Shin; Moon, Kyung-Sub; Seo, Jeong-Jin; Kim, In-Young; Jung, Tae-Young; Lee, Jung-Kil; Kang, Sam-Suk

2005-08-01

Recent developments in magnetic resonance (MR) technology now enable the use of MR venography, providing 3-dimensional (3D) images of intracranial venous structures. The purpose of this study was to assess the usefulness of 3D contrast-enhanced MR venography (CE MRV) in the evaluation of intracranial venous system for surgical planning of brain tumors. Forty patients underwent 3D CE MRV, as well as 25 patients, 2-dimensional (2D) time-of-flight (TOF) MR venography in axial and sagittal planes; and 10 patients, digital subtraction angiography. We determined the number of visualized sinuses and cortical veins. Degree of visualization of the intracranial venous system on 3D CE MRV was compared with that of 2D TOF MR venography and digital subtraction angiography as a standard. We also assessed the value of 3D CE MRV in the investigation of sinus occlusion or localization of cortical draining veins preoperatively. Superficial cortical veins and the dural sinus were better visualized on 3D CE MRV than on 2D TOF MR venography. Both MR venographic techniques visualized superior sagittal sinus, lateral sinus, sigmoid sinus, straight sinus, and internal cerebral vein and provided more detailed information by showing obstructed sinuses in brain tumors. Only 3D CE MRV showed superficial cortical draining veins. However, it was difficult to accurately evaluate the presence of cortical collateral venous drainage. Although we do not yet advocate MR venography to replace conventional angiography as the imaging standard for brain tumors, 3D CE MRV can be regarded as a valuable diagnostic method just in evaluating the status of major sinuses and localization of the cortical draining veins.

Series of Noncontrast Time-of-Flight Magnetic Resonance Angiographies to Identify Problems with Arteriovenous Fistula Maturation.

PubMed

Gonzalez, Aaron J; Casey, Kevin M; Drinkwine, Benjamin J; Weiss, Jeffrey S

2016-01-01

Successful maturation of arteriovenous fistulas (AVFs) remains a challenge for those managing patients with end-stage renal disease. Time-of-flight magnetic resonance angiography (TOF-MR) can be used to evaluate AVFs without the risk of radiation exposure, intravenous contrast, or reliance on the operator-dependent modality of color Doppler ultrasonography (CDUS). The objective of our study was to assess the utility of TOF-MR in the evaluation of nonmaturing AVFs and to identify the best clinical situations to use this technology. Consecutive patients with abnormal findings on CDUS or physical examination after AVF creation underwent 3-dimensional (3D) TOF-MR. Imaging was performed at 3 T with a scan acquisition time of approximately 15 min. The technique was similar to head and neck magnetic resonance angiography (MRA), except presaturation bands were not used, thereby allowing simultaneous visualization of both arterial and venous flow. A total of 19 TOF-MR studies were performed. Nineteen patients underwent imaging and were the focus of this study. Seventeen of 19 TOF-MR studies were of diagnostic quality and yielded findings which enabled the vascular surgeon to take corrective measures. Findings included inflow stenosis, anastomotic narrowing, venous outflow stenosis, and hemodynamically significant venous tributaries. Twelve of 17 patients required conventional digital subtraction angiography (DSA). The congruence rate between TOF-MR and DSA was 83.3%. Four patients (21%) avoided DSA and went directly to definitive surgical treatment including branch ligation (3) or new access (1). This is the first report in the literature of successful implementation of 3D TOF-MR to assist in identifying AVF maturation problems. This unique noninvasive imaging modality provides actionable images without contrast or radiation exposure and can obviate the need for invasive diagnostic procedures or provide an anatomic map for planning corrective intervention. Published by Elsevier Inc.

Identification and High-Resolution Imaging of α-Tocopherol from Human Cells to Whole Animals by TOF-SIMS Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bruinen, Anne L.; Fisher, Gregory L.; Balez, Rachelle; van der Sar, Astrid M.; Ooi, Lezanne; Heeren, Ron M. A.

2018-06-01

A unique method for identification of biomolecular components in different biological specimens, while preserving the capability for high speed 2D and 3D molecular imaging, is employed to investigate cellular response to oxidative stress. The employed method enables observing the distribution of the antioxidant α-tocopherol and other molecules in cellular structures via time-of-flight secondary ion mass spectrometry (TOF-SIMS (MS1)) imaging in parallel with tandem mass spectrometry (MS2) imaging, collected simultaneously. The described method is employed to examine a network formed by neuronal cells differentiated from human induced pluripotent stem cells (iPSCs), a model for investigating human neurons in vitro. The antioxidant α-tocopherol is identified in situ within different cellular layers utilizing a 3D TOF-SIMS tandem MS imaging analysis. As oxidative stress also plays an important role in mediating inflammation, the study was expanded to whole body tissue sections of M. marinum-infected zebrafish, a model organism for tuberculosis. The TOF-SIMS tandem MS imaging results reveal an increased presence of α-tocopherol in response to the pathogen. [Figure not available: see fulltext.

Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphism.

PubMed

Prakash, A; Sharma, C; Singh, A; Kumar Singh, P; Kumar, A; Hagen, F; Govender, N P; Colombo, A L; Meis, J F; Chowdhary, A

2016-03-01

Candida auris is a multidrug-resistant nosocomial bloodstream pathogen that has been reported from Asian countries and South Africa. Herein, we studied the population structure and genetic relatedness among 104 global C. auris isolates from India, South Africa and Brazil using multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RPB1, RPB2 and internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal DNA were sequenced for MLST. Further, genetic variation and proteomic assessment was carried out using AFLP and MALDI-TOF MS, respectively. Both MLST and AFLP typing clearly demarcated two major clusters comprising Indian and Brazilian isolates. However, the South African isolates were randomly distributed, suggesting different genotypes. MALDI-TOF MS spectral profiling also revealed evidence of geographical clustering but did not correlate fully with the genotyping methods. Notably, overall the population structure of C. auris showed evidence of geographical clustering by all the three techniques analysed. Antifungal susceptibility testing by the CLSI microbroth dilution method revealed that fluconazole had limited activity against 87% of isolates (MIC90, 64 mg/L). Also, MIC90 of AMB was 4 mg/L. Candida auris is emerging as an important yeast pathogen globally and requires reproducible laboratory methods for identification and typing. Evaluation of MALDI-TOF MS as a typing method for this yeast is warranted. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Single-Photon Detectors for Time-of-Flight Range Imaging

NASA Astrophysics Data System (ADS)

Stoppa, David; Simoni, Andrea

We live in a three-dimensional (3D) world and thanks to the stereoscopic vision provided by our two eyes, in combination with the powerful neural network of the brain we are able to perceive the distance of the objects. Nevertheless, despite the huge market volume of digital cameras, solid-state image sensors can capture only a two-dimensional (2D) projection, of the scene under observation, losing a variable of paramount importance, i.e., the scene depth. On the contrary, 3D vision tools could offer amazing possibilities of improvement in many areas thanks to the increased accuracy and reliability of the models representing the environment. Among the great variety of distance measuring techniques and detection systems available, this chapter will treat only the emerging niche of solid-state, scannerless systems based on the TOF principle and using a detector SPAD-based pixels. The chapter is organized into three main parts. At first, TOF systems and measuring techniques will be described. In the second part, most meaningful sensor architectures for scannerless TOF distance measurements will be analyzed, focusing onto the circuital building blocks required by time-resolved image sensors. Finally, a performance summary is provided and a perspective view for the near future developments of SPAD-TOF sensors is given.

MR angiography of the renal artery: comparison of breath-hold two-dimensional phase-contrast cine technique with the phased-array coil and breath-hold two-dimensional time-of-flight technique with the body coil.

PubMed

Masui, T; Takehara, Y; Igarashi, T; Ichijo, K; Takahashi, M; Kaneko, M; Nozaki, A

1997-07-01

Breath-hold 2D phase-contrast (PC) cine MR angiography with a phased-array coil and 2D time-of-flight (TOF) MR angiography were performed in the renal arteries and their findings were compared. Breath-hold 2D thin slice PC and TOF MR angiography were performed in 10 normal volunteers for renal arteries. A PC technique with k-space segmentation was utilized with the phased-array coil. A PC technique provided visualization of the renal artery more distally than a TOF technique (4.8 +/- 0.5 cm vs. 3.7 +/- 0.8 cm). With cardiac triggering, distal renal arteries were well demonstrated in PC MR angiography. On PC images, up- or downward movements of the mid to distal renal arteries with aortic pulsatility were recognized. The quality of the images was better with the PC than with the TOF technique (3.4 vs. 2.7). The mid to distal portions of the renal arteries translationally move with aortic pulsatility. To consistently visualize and evaluate them on MR angiography, cardiac triggering might be required to reduce the effects of pulsatile motions of the renal artery in the use of a phased-array coil.

Screening for illicit and medicinal drugs in whole blood using fully automated SPE and ultra-high-performance liquid chromatography with TOF-MS with data-independent acquisition.

PubMed

Pedersen, Anders Just; Dalsgaard, Petur Weihe; Rode, Andrej Jaroslav; Rasmussen, Brian Schou; Müller, Irene Breum; Johansen, Sys Stybe; Linnet, Kristian

2013-07-01

A broad forensic screening method for 256 analytes in whole blood based on a fully automated SPE robotic extraction and ultra-high-performance liquid chromatography (UHPLC) with TOF-MS with data-independent acquisition has been developed. The limit of identification was evaluated for all 256 compounds and 95 of these compounds were validated with regard to matrix effects, extraction recovery, and process efficiency. The limit of identification ranged from 0.001 to 0.1 mg/kg, and the process efficiency exceeded 50% for 73 of the 95 analytes. As an example of application, 1335 forensic traffic cases were analyzed with the presented screening method. Of these, 992 cases (74%) were positive for one or more traffic-relevant drugs above the Danish legal limits. Commonly abused drugs such as amphetamine, cocaine, and frequent types of benzodiazepines were the major findings. Nineteen less frequently encountered drugs were detected e.g. buprenorphine, butylone, cathine, fentanyl, lysergic acid diethylamide, m-chlorophenylpiperazine, 3,4-methylenedioxypyrovalerone, mephedrone, 4-methylamphetamine, p-fluoroamphetamine, and p-methoxy-N-methylamphetamine. In conclusion, using UHPLC-TOF-MS screening with data-independent acquisition resulted in the detection of common drugs of abuse as well as new designer drugs and more rarely occurring drugs. Thus, TOF-MS screening of blood samples constitutes a practical way for screening traffic cases, with the exception of δ-9-tetrahydrocannabinol, which should be handled in a separate method. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.).

PubMed

Wang, Aili; Liu, Li; Peng, Yanchun; Islam, Shahidul; Applebee, Marie; Appels, Rudi; Yan, Yueming; Ma, Wujun

2015-01-01

Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end-product quality attributes.

Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.)

PubMed Central

Islam, Shahidul; Applebee, Marie; Appels, Rudi; Yan, Yueming; Ma, Wujun

2015-01-01

Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end-product quality attributes. PMID:26407296

A novel PFIB sample preparation protocol for correlative 3D X-ray CNT and FIB-TOF-SIMS tomography.

PubMed

Priebe, Agnieszka; Audoit, Guillaume; Barnes, Jean-Paul

2017-02-01

We present a novel sample preparation method that allows correlative 3D X-ray Computed Nano-Tomography (CNT) and Focused Ion Beam Time-Of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS) tomography to be performed on the same sample. In addition, our invention ensures that samples stay unmodified structurally and chemically between the subsequent experiments. The main principle is based on modifying the topography of the X-ray CNT experimental setup before FIB-TOF-SIMS measurements by incorporating a square washer around the sample. This affects the distribution of extraction field lines and therefore influences the trajectories of secondary ions that are now guided more efficiently towards the detector. As the result, secondary ion detection is significantly improved and higher, i.e. statistically better, signals are obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

A follow-up study of autosomal dominant polycystic kidney disease with intracranial aneurysms using 3.0 T three-dimensional time-of-flight magnetic resonance angiography.

PubMed

Jiang, Tao; Wang, Peng; Qian, Yi; Zheng, Xuan; Xiao, Liaoyuan; Yu, Shengqiang; Liu, Shiyuan

2013-11-01

Autosomal dominant polycystic kidney disease (ADPKD) patients have an increased risk for intracranial aneurysms (IAs). Our aim was to screen and follow up the unruptured intracranial aneurysms (UIAs) detected by 3.0 T three-dimensional time-of-flight magnetic resonance angiography (3D-TOF MRA) in patients with ADPKD in order to evaluate the growth of UIAs and the value of 3D-TOF MRA. From 2011 to 2012, we followed up UIAs detected in 40 ADPKD patients who had MRA examinations with an interval of at least 36 months. All MRA examinations were performed on a 3T system (Achieva X-Series, Philips Medical Systems) with a Sense-Head-8 receiver head coil. The acquired data sets were transferred to a workstation (EWS, Philips Medical) to perform maximum intensity projection (MIP) and volume rendering (VR) with a specialized software package (Philips Medical). The size of UIAs was determined as the longest diameter in transverse or vertical measurement. UIAs that grew more than 20% were considered as enlarged. Fifty UIAs were found in 40 previously examined ADPKD patients who underwent 3.0 T 3D-TOF MRA follow-ups. No patients ever had treatment before the second examination. The longest diameter of all follow-up UIAs was less than 10mm and mean diameter was 3.64 ± 2.25 mm. UIAs in only 4 patients (10%) were considered as enlarged. None of the 50 IAs in the 40 ADPKD patients ruptured during the MRA follow-up period. 3.0 T 3D-TOF MRA was feasible for UIAs follow-up in ADPKD patients. The chance of enlargement and rupture of UIAs in ADPKD patients was not higher than in the general population. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

SPADAS: a high-speed 3D single-photon camera for advanced driver assistance systems

NASA Astrophysics Data System (ADS)

Bronzi, D.; Zou, Y.; Bellisai, S.; Villa, F.; Tisa, S.; Tosi, A.; Zappa, F.

2015-02-01

Advanced Driver Assistance Systems (ADAS) are the most advanced technologies to fight road accidents. Within ADAS, an important role is played by radar- and lidar-based sensors, which are mostly employed for collision avoidance and adaptive cruise control. Nonetheless, they have a narrow field-of-view and a limited ability to detect and differentiate objects. Standard camera-based technologies (e.g. stereovision) could balance these weaknesses, but they are currently not able to fulfill all automotive requirements (distance range, accuracy, acquisition speed, and frame-rate). To this purpose, we developed an automotive-oriented CMOS single-photon camera for optical 3D ranging based on indirect time-of-flight (iTOF) measurements. Imagers based on Single-photon avalanche diode (SPAD) arrays offer higher sensitivity with respect to CCD/CMOS rangefinders, have inherent better time resolution, higher accuracy and better linearity. Moreover, iTOF requires neither high bandwidth electronics nor short-pulsed lasers, hence allowing the development of cost-effective systems. The CMOS SPAD sensor is based on 64 × 32 pixels, each able to process both 2D intensity-data and 3D depth-ranging information, with background suppression. Pixel-level memories allow fully parallel imaging and prevents motion artefacts (skew, wobble, motion blur) and partial exposure effects, which otherwise would hinder the detection of fast moving objects. The camera is housed in an aluminum case supporting a 12 mm F/1.4 C-mount imaging lens, with a 40°×20° field-of-view. The whole system is very rugged and compact and a perfect solution for vehicle's cockpit, with dimensions of 80 mm × 45 mm × 70 mm, and less that 1 W consumption. To provide the required optical power (1.5 W, eye safe) and to allow fast (up to 25 MHz) modulation of the active illumination, we developed a modular laser source, based on five laser driver cards, with three 808 nm lasers each. We present the full characterization of the 3D automotive system, operated both at night and during daytime, in both indoor and outdoor, in real traffic, scenario. The achieved long-range (up to 45m), high dynamic-range (118 dB), highspeed (over 200 fps) 3D depth measurement, and high precision (better than 90 cm at 45 m), highlight the excellent performance of this CMOS SPAD camera for automotive applications.

Biomarkers of Aspergillus spores

NASA Astrophysics Data System (ADS)

Sulc, Miroslav; Peslova, Katerina; Zabka, Martin; Hajduch, Marian; Havlicek, Vladimir

2009-02-01

We applied both matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric and 1D sodium dodecylsulfate polyacrylamide gel electrophoretic (1D-PAGE) approaches for direct analysis of intact fungal spores of twenty four Aspergillus species. In parallel, we optimized various protocols for protein extraction from Aspergillus spores using acidic conditions, step organic gradient and variable sonication treatment. The MALDI-TOF mass spectra obtained from optimally prepared samples provided a reproducible fingerprint demonstrating the capability of the MALDI-TOF approach to type and characterize different fungal strains within the Aspergillus genus. Mass spectra of intact fungal spores provided signals mostly below 20 kDa. The minimum material amount represented 0.3 [mu]g (10,000 spores). Proteins with higher molecular weight were detected by 1D-PAGEE Eleven proteins were identified from three selected strains in the range 5-25 kDa by the proteomic approach. Hemolysin and hydrophobin have the highest relevance in host-pathogen interactions.

Contrast-enhanced time-resolved MRA for follow-up of intracranial aneurysms treated with the pipeline embolization device.

PubMed

Boddu, S R; Tong, F C; Dehkharghani, S; Dion, J E; Saindane, A M

2014-01-01

Endovascular reconstruction and flow diversion by using the Pipeline Embolization Device is an effective treatment for complex cerebral aneurysms. Accurate noninvasive alternatives to DSA for follow-up after Pipeline Embolization Device treatment are desirable. This study evaluated the accuracy of contrast-enhanced time-resolved MRA for this purpose, hypothesizing that contrast-enhanced time-resolved MRA will be comparable with DSA and superior to 3D-TOF MRA. During a 24-month period, 37 Pipeline Embolization Device-treated intracranial aneurysms in 26 patients underwent initial follow-up by using 3D-TOF MRA, contrast-enhanced time-resolved MRA, and DSA. MRA was performed on a 1.5T unit by using 3D-TOF and time-resolved imaging of contrast kinetics. All patients underwent DSA a median of 0 days (range, 0-68) after MRA. Studies were evaluated for aneurysm occlusion, quality of visualization of the reconstructed artery, and measurable luminal diameter of the Pipeline Embolization Device, with DSA used as the reference standard. The sensitivity, specificity, and positive and negative predictive values of contrast-enhanced time-resolved MRA relative to DSA for posttreatment aneurysm occlusion were 96%, 85%, 92%, and 92%. Contrast-enhanced time-resolved MRA demonstrated superior quality of visualization (P = .0001) and a higher measurable luminal diameter (P = .0001) of the reconstructed artery compared with 3D-TOF MRA but no significant difference compared with DSA. Contrast-enhanced time-resolved MRA underestimated the luminal diameter of the reconstructed artery by 0.965 ± 0.497 mm (27% ± 13%) relative to DSA. Contrast-enhanced time-resolved MRA is a reliable noninvasive method for monitoring intracranial aneurysms following flow diversion and vessel reconstruction by using the Pipeline Embolization Device. © 2014 by American Journal of Neuroradiology.

Predicting the timing properties of phosphor-coated scintillators using Monte Carlo light transport simulation

PubMed Central

Roncali, Emilie; Schmall, Jeffrey P.; Viswanath, Varsha; Berg, Eric; Cherry, Simon R.

2014-01-01

Current developments in positron emission tomography (PET) focus on improving timing performance for scanners with time-of-flight (TOF) capability, and incorporating depth-of-interaction (DOI) information. Recent studies have shown that incorporating DOI correction in TOF detectors can improve timing resolution, and that DOI also becomes more important in long axial field-of-view scanners. We have previously reported the development of DOI-encoding detectors using phosphor-coated scintillation crystals; here we study the timing properties of those crystals to assess the feasibility of providing some level of DOI information without significantly degrading the timing performance. We used Monte Carlo simulations to provide a detailed understanding of light transport in phosphor-coated crystals which cannot be fully characterized experimentally. Our simulations used a custom reflectance model based on 3D crystal surface measurements. Lutetium oxyorthosilicate (LSO) crystals were simulated with a phosphor coating in contact with the scintillator surfaces and an external diffuse reflector (teflon). Light output, energy resolution, and pulse shape showed excellent agreement with experimental data obtained on 3 × 3 × 10 mm3 crystals coupled to a photomultiplier tube (PMT). Scintillator intrinsic timing resolution was simulated with head-on and side-on configurations, confirming the trends observed experimentally. These results indicate that the model may be used to predict timing properties in phosphor-coated crystals and guide the coating for optimal DOI resolution/timing performance trade-off for a given crystal geometry. Simulation data suggested that a time stamp generated from early photoelectrons minimizes degradation of the timing resolution, thus making this method potentially more useful for TOF-DOI detectors than our initial experiments suggested. Finally, this approach could easily be extended to the study of timing properties in other scintillation crystals, with a range of treatments and materials attached to the surface. PMID:24694727

A Prospective, Matched Comparison Study of SUV Measurements From Time-of-Flight Versus Non-Time-of-Flight PET/CT Scanners.

PubMed

Thompson, Holly M; Minamimoto, Ryogo; Jamali, Mehran; Barkhodari, Amir; von Eyben, Rie; Iagaru, Andrei

2016-07-01

As quantitative F-FDG PET numbers and pooling of results from different PET/CT scanners become more influential in the management of patients, it becomes imperative that we fully interrogate differences between scanners to fully understand the degree of scanner bias on the statistical power of studies. Participants with body mass index (BMI) greater than 25, scheduled on a time-of-flight (TOF)-capable PET/CT scanner, had a consecutive scan on a non-TOF-capable PET/CT scanner and vice versa. SUVmean in various tissues and SUVmax of malignant lesions were measured from both scans, matched to each subject. Data were analyzed using a mixed-effects model, and statistical significance was determined using equivalence testing, with P < 0.05 being significant. Equivalence was established in all baseline organs, except the cerebellum, matched per patient between scanner types. Mixed-effects method analysis of lesions, repeated between scan types and matched per patient, demonstrated good concordance between scanner types. Patients could be scanned on either a TOF or non-TOF-capable PET/CT scanner without clinical compromise to quantitative SUV measurements.

Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat.

PubMed

Liu, Li; Ikeda, Tatsuya M; Branlard, Gerard; Peña, Roberto J; Rogers, William J; Lerner, Silvia E; Kolman, María A; Xia, Xianchun; Wang, Linhai; Ma, Wujun; Appels, Rudi; Yoshida, Hisashi; Wang, Aili; Yan, Yueming; He, Zhonghu

2010-06-24

Low-molecular-weight glutenin subunits (LMW-GS) play a crucial role in determining end-use quality of common wheat by influencing the viscoelastic properties of dough. Four different methods - sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE, IEF x SDS-PAGE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and polymerase chain reaction (PCR), were used to characterize the LMW-GS composition in 103 cultivars from 12 countries. At the Glu-A3 locus, all seven alleles could be reliably identified by 2-DE and PCR. However, the alleles Glu-A3e and Glu-A3d could not be routinely distinguished from Glu-A3f and Glu-A3g, respectively, based on SDS-PAGE, and the allele Glu-A3a could not be differentiated from Glu-A3c by MALDI-TOF-MS. At the Glu-B3 locus, alleles Glu-B3a, Glu-B3b, Glu-B3c, Glu-B3g, Glu-B3h and Glu-B3j could be clearly identified by all four methods, whereas Glu-B3ab, Glu-B3ac, Glu-B3ad could only be identified by the 2-DE method. At the Glu-D3 locus, allelic identification was problematic for the electrophoresis based methods and PCR. MALDI-TOF-MS has the potential to reliably identify the Glu-D3 alleles. PCR is the simplest, most accurate, lowest cost, and therefore recommended method for identification of Glu-A3 and Glu-B3 alleles in breeding programs. A combination of methods was required to identify certain alleles, and would be especially useful when characterizing new alleles. A standard set of 30 cultivars for use in future studies was chosen to represent all LMW-GS allelic variants in the collection. Among them, Chinese Spring, Opata 85, Seri 82 and Pavon 76 were recommended as a core set for use in SDS-PAGE gels. Glu-D3c and Glu-D3e are the same allele. Two new alleles, namely, Glu-D3m in cultivar Darius, and Glu-D3n in Fengmai 27, were identified by 2-DE. Utilization of the suggested standard cultivar set, seed of which is available from the CIMMYT and INRA Clermont-Ferrand germplasm collections, should also promote information sharing in the identification of individual LMW-GS and thus provide useful information for quality improvement in common wheat.

MR angiography fusion technique for treatment planning of intracranial arteriovenous malformations.

PubMed

McGee, Kiaran P; Ivanovic, Vladimir; Felmlee, Joel P; Meyer, Fredrick B; Pollock, Bruce E; Huston, John

2006-03-01

To develop an image fusion technique using elliptical centric contrast-enhanced (CE) MR angiography (MRA) and three-dimensional (3D) time-of-flight (TOF) acquisitions for radiosurgery treatment planning of arteriovenous malformations (AVMs). CE and 3D-TOF MR angiograms with disparate in-plane fields of view (FOVs) were acquired, followed by k-space reformatting to provide equal voxel dimensions. Spatial domain addition was performed to provide a third, fused data volume. Spatial distortion was evaluated on an MRA phantom and provided slice-dependent and global distortion along the three physical dimensions of the MR scanner. In vivo validation was performed on 10 patients with intracranial AVMs prior to their conventional angiogram on the day of gamma knife radiosurgery. Spatial distortion in the phantom within a volume of 14 x 14 x 3.2 cm(3) was less than +/-1 mm (+/-1 standard deviation (SD)) for CE and 3D-TOF data sets. Fused data volumes were successfully generated for all 10 patients. Image fusion can be used to obtain high-resolution CE-MRA images of intracranial AVMs while keeping the fiducial markers needed for gamma knife radiosurgery planning. The spatial fidelity of these data is within the tolerance acceptable for daily quality control (QC) purposes and gamma knife treatment planning. (c) 2006 Wiley-Liss, Inc.

Contrast-Enhanced and Time-of-Flight MRA at 3T Compared with DSA for the Follow-Up of Intracranial Aneurysms Treated with the WEB Device.

PubMed

Timsit, C; Soize, S; Benaissa, A; Portefaix, C; Gauvrit, J-Y; Pierot, L

2016-09-01

Imaging follow-up at 3T of intracranial aneurysms treated with the WEB Device has not been evaluated yet. Our aim was to assess the diagnostic accuracy of 3D-time-of-flight MRA and contrast-enhanced MRA at 3T against DSA, as the criterion standard, for the follow-up of aneurysms treated with the Woven EndoBridge (WEB) system. From June 2011 to December 2014, patients treated with the WEB in our institution, then followed for ≥6 months after treatment by MRA at 3T (3D-TOF-MRA and contrast-enhanced MRA) and DSA within 48 hours were included. Aneurysm occlusion was assessed with a simplified 2-grade scale (adequate occlusion [total occlusion + neck remnant] versus aneurysm remnant). Interobserver and intermodality agreement was evaluated by calculating the linear weighted κ. MRA test characteristics and predictive values were calculated from a 2 × 2 contingency table, by using DSA data as the standard of reference. Twenty-six patients with 26 WEB-treated aneurysms were included. The interobserver reproducibility was good with DSA (κ = 0.71) and contrast-enhanced-MRA (κ = 0.65) compared with moderate with 3D-TOF-MRA (κ = 0.47). Intermodality agreement with DSA was fair with both contrast-enhanced MRA (κ = 0.36) and 3D-TOF-MRA (κ = 0.36) for the evaluation of total occlusion. For aneurysm remnant detection, the prevalence was low (15%), on the basis of DSA, and both MRA techniques showed low sensitivity (25%), high specificity (100%), very good positive predictive value (100%), and very good negative predictive value (88%). Despite acceptable interobserver reproducibility and predictive values, the low sensitivity of contrast-enhanced MRA and 3D-TOF-MRA for aneurysm remnant detection suggests that MRA is a useful screening procedure for WEB-treated aneurysms, but similar to stents and flow diverters, DSA remains the criterion standard for follow-up. © 2016 by American Journal of Neuroradiology.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

The 3H(d,γ)5He Reaction for Ec.m. ≤ 300 keV

NASA Astrophysics Data System (ADS)

Parker, C. E.; Brune, C. R.; Massey, T. N.; O'Donnell, J. E.; Richard, A. L.; Sayre, D. B.

2016-03-01

The 3H(d, γ)5He reaction has been measured using a 500-keV pulsed deuteron beam incident on a stopping titanium tritide target at Ohio University's Edwards Accelerator Laboratory. The time-of-flight (TOF) technique has been used to distinguish the γ-rays from neutrons detected in the bismuth germinate (BGO) γ-ray detector. A stilbene scintillator and an NE-213 scintillator have been used to detect the neutrons from the 3H(d, n)4He reaction using both the pulse-shape discrimination and TOF techniques. A newly-designed target holder with a silicon surface barrier detector to simultaneously measure α-particles to normalize the neutron count was incorporated for subsequent measurements. The γ-rays have been measured at laboratory angles of 0°, 45°, 90°, and 135°. Information about the γ-ray energy distribution for the unbound ground state and first excited state of 5He can be obtained experimentally by comparing the BGO data to Monte Carlo simulations. The 3H(d, γ)/3H(d, n) branching ratio has also been determined.

3D surface reconstruction for laparoscopic computer-assisted interventions: comparison of state-of-the-art methods

NASA Astrophysics Data System (ADS)

Groch, A.; Seitel, A.; Hempel, S.; Speidel, S.; Engelbrecht, R.; Penne, J.; Höller, K.; Röhl, S.; Yung, K.; Bodenstedt, S.; Pflaum, F.; dos Santos, T. R.; Mersmann, S.; Meinzer, H.-P.; Hornegger, J.; Maier-Hein, L.

2011-03-01

One of the main challenges related to computer-assisted laparoscopic surgery is the accurate registration of pre-operative planning images with patient's anatomy. One popular approach for achieving this involves intraoperative 3D reconstruction of the target organ's surface with methods based on multiple view geometry. The latter, however, require robust and fast algorithms for establishing correspondences between multiple images of the same scene. Recently, the first endoscope based on Time-of-Flight (ToF) camera technique was introduced. It generates dense range images with high update rates by continuously measuring the run-time of intensity modulated light. While this approach yielded promising results in initial experiments, the endoscopic ToF camera has not yet been evaluated in the context of related work. The aim of this paper was therefore to compare its performance with different state-of-the-art surface reconstruction methods on identical objects. For this purpose, surface data from a set of porcine organs as well as organ phantoms was acquired with four different cameras: a novel Time-of-Flight (ToF) endoscope, a standard ToF camera, a stereoscope, and a High Definition Television (HDTV) endoscope. The resulting reconstructed partial organ surfaces were then compared to corresponding ground truth shapes extracted from computed tomography (CT) data using a set of local and global distance metrics. The evaluation suggests that the ToF technique has high potential as means for intraoperative endoscopic surface registration.

Triple Quadrupole Versus High Resolution Quadrupole-Time-of-Flight Mass Spectrometry for Quantitative LC-MS/MS Analysis of 25-Hydroxyvitamin D in Human Serum

NASA Astrophysics Data System (ADS)

Geib, Timon; Sleno, Lekha; Hall, Rabea A.; Stokes, Caroline S.; Volmer, Dietrich A.

2016-08-01

We describe a systematic comparison of high and low resolution LC-MS/MS assays for quantification of 25-hydroxyvitamin D3 in human serum. Identical sample preparation, chromatography separations, electrospray ionization sources, precursor ion selection, and ion activation were used; the two assays differed only in the implemented final mass analyzer stage; viz. high resolution quadrupole-quadrupole-time-of-flight (QqTOF) versus low resolution triple quadrupole instruments. The results were assessed against measured concentration levels from a routine clinical chemiluminescence immunoassay. Isobaric interferences prevented the simple use of TOF-MS spectra for extraction of accurate masses and necessitated the application of collision-induced dissociation on the QqTOF platform. The two mass spectrometry assays provided very similar analytical figures of merit, reflecting the lack of relevant isobaric interferences in the MS/MS domain, and were successfully applied to determine the levels of 25-hydroxyvitamin D for patients with chronic liver disease.

Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization.

PubMed

Fagerquist, Clifton K

2017-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in the MS peaks that collectively constitute the MS 'fingerprint'. This review/perspective is intended to explore this topic in greater detail in the hopes that it may spur interest and further research in this area. Areas covered: This paper examines the recent literature on utilizing MALDI-TOF for bacterial identification. Critical works highlighting protein biomarker identification of bacteria, arguments for and against protein biomarker identification, proteomic approaches to biomarker identification, emergence of MALDI-TOF-TOF platforms and their use for top-down proteomic identification of bacterial proteins, protein denaturation and its effect on protein ion fragmentation, collision cross-sections and energy deposition during desorption/ionization are also explored. Expert commentary: MALDI-TOF and TOF-TOF mass spectrometry platforms will continue to provide chemical analyses that are rapid, cost-effective and high throughput. These instruments have proven their utility in the taxonomic identification of pathogenic bacteria at the genus and species level and are poised to more fully characterize these microorganisms to the benefit of clinical microbiology, food safety and other fields.

Multidimensional gas chromatography in combination with accurate mass, tandem mass spectrometry, and element-specific detection for identification of sulfur compounds in tobacco smoke.

PubMed

Ochiai, Nobuo; Mitsui, Kazuhisa; Sasamoto, Kikuo; Yoshimura, Yuta; David, Frank; Sandra, Pat

2014-09-05

A method is developed for identification of sulfur compounds in tobacco smoke extract. The method is based on large volume injection (LVI) of 10μL of tobacco smoke extract followed by selectable one-dimensional ((1)D) or two-dimensional ((2)D) gas chromatography (GC) coupled to a hybrid quadrupole time-of-flight mass spectrometer (Q-TOF-MS) using electron ionization (EI) and positive chemical ionization (PCI), with parallel sulfur chemiluminescence detection (SCD). In order to identify each individual sulfur compound, sequential heart-cuts of 28 sulfur fractions from (1)D GC to (2)D GC were performed with the three MS detection modes (SCD/EI-TOF-MS, SCD/PCI-TOF-MS, and SCD/PCI-Q-TOF-MS). Thirty sulfur compounds were positively identified by MS library search, linear retention indices (LRI), molecular mass determination using PCI accurate mass spectra, formula calculation using EI and PCI accurate mass spectra, and structure elucidation using collision activated dissociation (CAD) of the protonated molecule. Additionally, 11 molecular formulas were obtained for unknown sulfur compounds. The determined values of the identified and unknown sulfur compounds were in the range of 10-740ngmg total particulate matter (TPM) (RSD: 1.2-12%, n=3). Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Characterizing Neutron Diagnostics on the nTOF Line at SUNY Geneseo

NASA Astrophysics Data System (ADS)

Harrison, Hannah; Seppala, Hannah; Visca, Hannah; Wakwella, Praveen; Fletcher, Kurt; Padalino, Stephen; Forrest, Chad; Regan, Sean; Sangster, Craig

2016-10-01

Charged particle beams from SUNY Geneseo's 1.7 MV Tandem Pelletron Accelerator induce nuclear reactions that emit neutrons ranging from 0.5 to 17.9 MeV via 2H(d,n)3He and 11B(d,n)12C. This adjustable neutron source can be used to calibrate ICF and HEDP neutron scintillators for ICF diagnostics. However, gamma rays and muons, which are often present during an accelerator-based calibration, are difficult to differentiate from neutron signals in scintillators. To mitigate this problem, a new neutron time-of-flight (nTOF) line has been constructed. The nTOF timing is measured using the associated particle technique. A charged particle produced by the nuclear reaction serves as a start signal, while its associated neutron is the stop signal. Each reaction is analyzed event-by-event to determine whether the scintillator signal was generated by a neutron, gamma or muon. Using this nTOF technique, the neutron response for different scintillation detectors can be determined. Funded in part by a LLE contract through the DOE.

Adenosine A(2A) receptor antagonists are broad facilitators of antinicotinic neuromuscular blockade monitored either with 2 Hz train-of-four or 50 Hz tetanic stimuli.

PubMed

Pereira, Monalisa W; Correia-de-Sá, Paulo; Alves-Do-Prado, Wilson

2012-10-01

1. The 2 Hz train-of-four ratio (TOF(ratio)) is used to monitor the degree of patient curarization. Using a rat phrenic nerve-hemidiaphragm preparation, we showed that antinicotinic agents, such as hexamethonium, d-tubocurarine and pancuronium, but not cisatracurium, decreased contractions produced by physiological nerve activity patterns (50 Hz) more efficiently than those caused by 2 Hz trains. Uncertainty about the usefulness of the TOF(ratio) to control safe recovery from curarization prompted us to investigate the muscarinic and adenosine neuromodulation of tetanic (50 Hz) fade induced by antinicotinic agents at concentrations that cause a 25% reduction in the TOF(ratio) (TOF(fade)). 2. Tetanic fade caused by d-tubocurarine (1.1 μmol/L), pancuronium (3 μmol/L) and hexamethonium (5.47 mmol/L) was attenuated by blocking presynaptic inhibitory muscarinic M(2) and adenosine A(1) receptors with methoctramine (1 μmol/L) and 1,3-dipropyl-8-cyclopentylxanthine (2.5 nmol/L), respectively. These compounds enhanced rather than decreased tetanic fade induced by cisatracurium (2.2 μmol/L), but they consistently attenuated cisatracurium-induced TOF(fade). The effect of the M(1) receptor antagonist pirenzepine (10 nmol/L) on fade produced by antinicotinic agents at 50 Hz was opposite to that observed with TOF stimulation. Blockade of adenosine A(2A) receptors with ZM 241385 (10 nmol/L) attenuated TOF(fade) caused by all antinicotinic drugs tested, with the exception of the 'pure' presynaptic nicotinic antagonist hexamethonium. ZM 241385 was the only compound tested in this series that facilitated recovery from tetanic fade produced by cisatracurium. 3. The data suggest that distinct antinicotinic relaxants interfere with fine-tuning neuromuscular adaptations to motor nerve stimulation patterns via activation of presynaptic muscarinic and adenosine receptors. These results support the use of A(2A) receptor antagonists together with atropine to facilitate recovery from antinicotinic neuromuscular blockade. © 2012 The Authors Clinical and Experimental Pharmacology and Physiology © 2012 Wiley Publishing Asia Pty Ltd.

Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species.

PubMed

Lacroix, C; Gicquel, A; Sendid, B; Meyer, J; Accoceberry, I; François, N; Morio, F; Desoubeaux, G; Chandenier, J; Kauffmann-Lacroix, C; Hennequin, C; Guitard, J; Nassif, X; Bougnoux, M-E

2014-02-01

Candida spp. are responsible for severe infections in immunocompromised patients and those undergoing invasive procedures. The accurate identification of Candida species is important because emerging species can be associated with various antifungal susceptibility spectra. Conventional methods have been developed to identify the most common pathogens, but have often failed to identify uncommon species. Several studies have reported the efficiency of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of clinically relevant Candida species. In this study, we evaluated two commercially available MALDI-TOF systems, Andromas™ and Bruker Biotyper™, for Candida identification in routine diagnosis. For this purpose, we investigated 1383 Candida isolates prospectively collected in eight hospital laboratories during routine practice. MALDI-TOF MS results were compared with those obtained using conventional phenotypic methods. Analysis of rDNA gene sequences with internal transcribed regions or D1-D2 regions is considered the reference standard for identification. Both MALDI-TOF MS systems could accurately identify 98.3% of the isolates at the species level (1359/1383 for Andromas™; 1360/1383 for Bruker Biotyper™) vs. 96.5% for conventional techniques. Furthermore, whereas conventional methods failed to identify rare or emerging species, these were correctly identified by MALDI-TOF MS. Both MALDI-TOF MS systems are accurate and cost-effective alternatives to conventional methods for mycological identification of clinically relevant Candida species and should improve the diagnosis of fungal infections as well as patient management. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Three-dimensional magnetic resonance imaging based on time-of-flight magnetic resonance angiography for superficial cerebral arteriovenous malformation--technical note.

PubMed

Murata, Takahiro; Horiuchi, Tetsuyoshi; Rahmah, Nunung Nur; Sakai, Keiichi; Hongo, Kazuhiro

2011-01-01

Direct surgery remains important for the treatment of superficial cerebral arteriovenous malformation (AVM). Surgical planning on the basis of careful analysis from various neuroimaging modalities can aid in resection of superficial AVM with favorable outcome. Three-dimensional (3D) magnetic resonance (MR) imaging reconstructed from time-of-flight (TOF) MR angiography was developed as an adjunctive tool for surgical planning of superficial AVM. 3-T TOF MR imaging without contrast medium was performed preoperatively in patients with superficial AVM. The images were imported into OsiriX imaging software and the 3D reconstructed MR image was produced using the volume rendering method. This 3D MR image could clearly visualize the surface angioarchitecture of the AVM with the surrounding brain on a single image, and clarified feeding arteries including draining veins and the relationship with sulci or fissures surrounding the nidus. 3D MR image of the whole AVM angioarchitecture was also displayed by skeletonization of the surrounding brain. Preoperative 3D MR image corresponded to the intraoperative view. Feeders on the brain surface were easily confirmed and obliterated during surgery, with the aid of the 3D MR images. 3D MR imaging for surgical planning of superficial AVM is simple and noninvasive to perform, enhances intraoperative orientation, and is helpful for successful resection.

Temporal consistent depth map upscaling for 3DTV

NASA Astrophysics Data System (ADS)

Schwarz, Sebastian; Sjöström, Mârten; Olsson, Roger

2014-03-01

The ongoing success of three-dimensional (3D) cinema fuels increasing efforts to spread the commercial success of 3D to new markets. The possibilities of a convincing 3D experience at home, such as three-dimensional television (3DTV), has generated a great deal of interest within the research and standardization community. A central issue for 3DTV is the creation and representation of 3D content. Acquiring scene depth information is a fundamental task in computer vision, yet complex and error-prone. Dedicated range sensors, such as the Time­ of-Flight camera (ToF), can simplify the scene depth capture process and overcome shortcomings of traditional solutions, such as active or passive stereo analysis. Admittedly, currently available ToF sensors deliver only a limited spatial resolution. However, sophisticated depth upscaling approaches use texture information to match depth and video resolution. At Electronic Imaging 2012 we proposed an upscaling routine based on error energy minimization, weighted with edge information from an accompanying video source. In this article we develop our algorithm further. By adding temporal consistency constraints to the upscaling process, we reduce disturbing depth jumps and flickering artifacts in the final 3DTV content. Temporal consistency in depth maps enhances the 3D experience, leading to a wider acceptance of 3D media content. More content in better quality can boost the commercial success of 3DTV.

Contrast Enhancement in TOF cerebral angiography at 7 T using Saturation and MT pulses under SAR constraints: impact of VERSE and sparse pulses

PubMed Central

Schmitter, Sebastian; Bock, Michael; Johst, Sören; Auerbach, Edward J.; Uğurbil, Kâmil; Van de Moortele, Pierre-François

2011-01-01

Cerebral 3D time of flight (TOF) angiography significantly benefits from ultra high fields, mainly due to higher SNR and to longer T1 relaxation time of static brain tissues, however, SAR significantly increases with B0. Thus, additional RF pulses commonly used at lower field strengths to improve TOF contrast such as saturation of venous signal and improved background suppression by magnetization transfer typically cannot be used at higher fields. In this work we aimed at reducing SAR for each RF pulse category in a TOF sequence. We use the VERSE principle for the slab selective TOF excitation as well as the venous saturation RF pulses. Additionally, MT pulses are implemented by sparsely applying the pulses only during acquisition of the central k-space lines to limit their SAR contribution. Image quality, angiographic contrast and SAR reduction were investigated as a function of VERSE parameters and of the total number of MT pulses applied. Based on these results, a TOF protocol was generated that increases the angiographic contrast by more than 50% and reduces subcutaneous fat signal while keeping the resulting SAR within regulatory limits. PMID:22139829

Identification and Characterization of Cell Wall Proteins of a Toxic Dinoflagellate Alexandrium catenella Using 2-D DIGE and MALDI TOF-TOF Mass Spectrometry

PubMed Central

Wang, Da-Zhi; Dong, Hong-Po; Li, Cheng; Xie, Zhang-Xian; Lin, Lin; Hong, Hua-Sheng

2011-01-01

The cell wall is an important subcellular component of dinoflagellate cells with regard to various aspects of cell surface-associated ecophysiology, but the full range of cell wall proteins (CWPs) and their functions remain to be elucidated. This study identified and characterized CWPs of a toxic dinoflagellate, Alexandrium catenella, using a combination of 2D fluorescence difference gel electrophoresis (DIGE) and MALDI TOF-TOF mass spectrometry approaches. Using sequential extraction and temperature shock methods, sequentially extracted CWPs and protoplast proteins, respectively, were separated from A. catenella. From the comparison between sequentially extracted CWPs labeled with Cy3 and protoplast proteins labeled with Cy5, 120 CWPs were confidently identified in the 2D DIGE gel. These proteins gave positive identification of protein orthologues in the protein database using de novo sequence analysis and homology-based search. The majority of the prominent CWPs identified were hypothetical or putative proteins with unknown function or no annotation, while cell wall modification enzymes, cell wall structural proteins, transporter/binding proteins, and signaling and defense proteins were tentatively identified in agreement with the expected role of the extracellular matrix in cell physiology. This work represents the first attempt to investigate dinoflagellate CWPs and provides a potential tool for future comprehensive characterization of dinoflagellate CWPs and elucidation of their physiological functions. PMID:21904561

Human machine interface by using stereo-based depth extraction

NASA Astrophysics Data System (ADS)

Liao, Chao-Kang; Wu, Chi-Hao; Lin, Hsueh-Yi; Chang, Ting-Ting; Lin, Tung-Yang; Huang, Po-Kuan

2014-03-01

The ongoing success of three-dimensional (3D) cinema fuels increasing efforts to spread the commercial success of 3D to new markets. The possibilities of a convincing 3D experience at home, such as three-dimensional television (3DTV), has generated a great deal of interest within the research and standardization community. A central issue for 3DTV is the creation and representation of 3D content. Acquiring scene depth information is a fundamental task in computer vision, yet complex and error-prone. Dedicated range sensors, such as the Time­ of-Flight camera (ToF), can simplify the scene depth capture process and overcome shortcomings of traditional solutions, such as active or passive stereo analysis. Admittedly, currently available ToF sensors deliver only a limited spatial resolution. However, sophisticated depth upscaling approaches use texture information to match depth and video resolution. At Electronic Imaging 2012 we proposed an upscaling routine based on error energy minimization, weighted with edge information from an accompanying video source. In this article we develop our algorithm further. By adding temporal consistency constraints to the upscaling process, we reduce disturbing depth jumps and flickering artifacts in the final 3DTV content. Temporal consistency in depth maps enhances the 3D experience, leading to a wider acceptance of 3D media content. More content in better quality can boost the commercial success of 3DTV.

A 3D image sensor with adaptable charge subtraction scheme for background light suppression

NASA Astrophysics Data System (ADS)

Shin, Jungsoon; Kang, Byongmin; Lee, Keechang; Kim, James D. K.

2013-02-01

We present a 3D ToF (Time-of-Flight) image sensor with adaptive charge subtraction scheme for background light suppression. The proposed sensor can alternately capture high resolution color image and high quality depth map in each frame. In depth-mode, the sensor requires enough integration time for accurate depth acquisition, but saturation will occur in high background light illumination. We propose to divide the integration time into N sub-integration times adaptively. In each sub-integration time, our sensor captures an image without saturation and subtracts the charge to prevent the pixel from the saturation. In addition, the subtraction results are cumulated N times obtaining a final result image without background illumination at full integration time. Experimental results with our own ToF sensor show high background suppression performance. We also propose in-pixel storage and column-level subtraction circuit for chiplevel implementation of the proposed method. We believe the proposed scheme will enable 3D sensors to be used in out-door environment.

Sensors for 3D Imaging: Metric Evaluation and Calibration of a CCD/CMOS Time-of-Flight Camera.

PubMed

Chiabrando, Filiberto; Chiabrando, Roberto; Piatti, Dario; Rinaudo, Fulvio

2009-01-01

3D imaging with Time-of-Flight (ToF) cameras is a promising recent technique which allows 3D point clouds to be acquired at video frame rates. However, the distance measurements of these devices are often affected by some systematic errors which decrease the quality of the acquired data. In order to evaluate these errors, some experimental tests on a CCD/CMOS ToF camera sensor, the SwissRanger (SR)-4000 camera, were performed and reported in this paper. In particular, two main aspects are treated: the calibration of the distance measurements of the SR-4000 camera, which deals with evaluation of the camera warm up time period, the distance measurement error evaluation and a study of the influence on distance measurements of the camera orientation with respect to the observed object; the second aspect concerns the photogrammetric calibration of the amplitude images delivered by the camera using a purpose-built multi-resolution field made of high contrast targets.

Fusion of magnetic resonance angiography and magnetic resonance imaging for surgical planning for meningioma--technical note.

PubMed

Kashimura, Hiroshi; Ogasawara, Kuniaki; Arai, Hiroshi; Beppu, Takaaki; Inoue, Takashi; Takahashi, Tsutomu; Matsuda, Koichi; Takahashi, Yujiro; Fujiwara, Shunrou; Ogawa, Akira

2008-09-01

A fusion technique for magnetic resonance (MR) angiography and MR imaging was developed to help assess the peritumoral angioarchitecture during surgical planning for meningioma. Three-dimensional time-of-flight (3D-TOF) and 3D-spoiled gradient recalled (SPGR) datasets were obtained from 10 patients with intracranial meningioma, and fused using newly developed volume registration and visualization software. Maximum intensity projection (MIP) images from 3D-TOF MR angiography and axial SPGR MR imaging were displayed at the same time on the monitor. Selecting a vessel on the real-time MIP image indicated the corresponding points on the axial image automatically. Fusion images showed displacement of the anterior cerebral or middle cerebral artery in 7 patients and encasement of the anterior cerebral arteries in 1 patient, with no relationship between the main arterial trunk and tumor in 2 patients. Fusion of MR angiography and MR imaging can clarify relationships between the intracranial vasculature and meningioma, and may be helpful for surgical planning for meningioma.

Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

EPA Science Inventory

Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

Identification of inflammation-related proteins in a murine colitis model by 2D fluorescence difference gel electrophoresis and mass spectrometry.

PubMed

Naito, Yuji; Takagi, Tomohisa; Okada, Hitomi; Omatsu, Tatsushi; Mizushima, Katsura; Handa, Osamu; Kokura, Satoshi; Ichikawa, Hiroshi; Fujiwake, Hideshi; Yoshikawa, Toshikazu

2010-05-01

The aim of this study was to identify new intestinal proteins potentially associated with acute inflammation using proteomic profiling of an in vivo mice model of ulcerative colitis. 2D fluorescence difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight spectrometer (MALDI-TOF) peptide mass fingerprinting were used to determine differentially expressed proteins between normal and inflamed intestinal mucosa. Acute colitis was induced by 8.0% dextran sodium sulfate (DSS) given p.o. for 7 days. Among a total of seven protein spots showing differential expression, we identified five different proteins, of which two were upregulated and three downregulated in colitis in comparison to normal mucosa, using the MASCOT search engine. 3-Hydroxy-3-methylglutaryl-coenzyme A synthase 2 and serpin b1a were upregulated proteins, and protein disulfide-isomerase A3, peroxiredoxin-6 and vimentin were identified as downregulated proteins. These identified proteins may be responsible for the development of the intestinal inflammation. 2D-DIGE and MALDI-TOF mass spectrometry are useful in the search for the differentially expressed proteins.

Spectroscopic, electrochemical and photovoltaic properties of Pt(ii) and Pd(ii) complexes of a chelating 1,10-phenanthroline appended perylene diimide.

PubMed

Işık Büyükekşi, Sebile; Şengül, Abdurrahman; Erdönmez, Seda; Altındal, Ahmet; Orman, Efe Baturhan; Özkaya, Ali Rıza

2018-02-20

In this study, a bis-chelating bridging perylene diimide ditopic ligand, namely N,N'-di(1,10-phenanthroline)-1,6,7,12-tetrakis-(4-methoxyphenoxy)perylene tetracarboxylic acid diimide (1), was synthesized and characterized. Further reactions of 1 with d 8 metal ions such as Pt(ii) and Pd(ii) having preferential square-planar geometry afforded the novel triads [(Cl 2 )M(ii)-(1)-M(ii)(Cl 2 )] where M(ii) = Pt(ii) (2), and Pd(ii) (3), respectively. The isolated triads and the key precursor were fully characterized by FT-IR, 1D-NMR ( 1 H NMR and 13 C DEPT NMR), 2D-NMR ( 1 H- 1 H COSY, 1 H- 13 C HSQC, 1 H- 13 C HMBC), MALDI-TOF mass and UV/Vis spectroscopy. The electrochemical properties of 1, 2 and 3 were investigated by cyclic voltammetry as well as in situ spectroelectrochemistry and also in situ electrocolorimetric measurements. These compounds were shown to exhibit net colour changes suitable for electrochromic applications. The compounds exhibited remarkably narrow HOMO-LUMO gaps, leading to their ease of reduction at low negative potentials. More importantly, dye-sensitized solar cells (DSSCs) were also fabricated using 1-3 to clarify the potential use of these complexes as a sensitizer. Analysis of the experimental data indicated that 2 has good potential as a sensitizer material for DSSCs.

Experimental assessment of valve performance in healthy and diseased right ventricular outflow tracts using magnetic resonance velocimetry

NASA Astrophysics Data System (ADS)

Schiavone, Nicole; Elkins, Christopher; McElhinney, Doff; Eaton, John K.; Marsden, Alison

2017-11-01

Tetralogy of Fallot (ToF), the most common type of cyanotic congenital heart defect, affects 1 in every 2500 newborns annually and typically requires surgical repair of the right ventricular outflow tract (RVOT) and placement of an artificial pulmonary valve. All artificial valves are subject to dysfunction, but their longevity is highly variable. Clinical observation reveals large variations in RVOT anatomy in ToF patients, which may affect longevity. This work aims to experimentally assess the performance of artificial pulmonary valves in anatomically realistic healthy and diseased RVOT geometries using magnetic resonance velocimetry (MRV). With MRV, we can capture 3D, three-component, phase-averaged velocity fields in 3D printed RVOT geometries. The experiment is designed to ensure physiological flow rate and pressure waveforms, while the RVOT geometries are based on anatomies seen clinically in ToF patients. Two models are used in the current work: an idealized RVOT based on healthy subjects aged eleven to thirteen and a diseased geometry with a dilation of 150% in vessel diameter downstream of the pulmonary valve. We will also present preliminary rigid-wall blood flow simulations in each model, towards the ultimate goal of experimental validation of valve simulations.

Robotic Tactile Sensing

DTIC Science & Technology

1988-06-08

develop a working experi- tal system which could demonstrate dexterous manipulation in a robotic assembly task. Th ,pe of work can generally be divided into...D Raviv discukse the development, implementation, and experimental evaluation tof a new method for the reconstruction of 3D images from 2D vision data...Research supervision by K. Loparo A. "Moving Shadows Methods for Inferring Three Dimensional Surfaces," D. Raviv , Ph.D. Thesis B. "Robotic Adaptive

Construction of the optical part of a time-of-flight detector prototype for the AFP detector

DOE PAGES

Nozka, L.; Adamczyk, L.; Avoni, G.; ...

2016-11-22

We present the construction of the optical part of the ToF (time-of-flight) subdetector prototype for the AFP (ATLAS Forward Proton) detector. The ToF detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgrounds that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from themore » ToF allows the proton tagger to operate at the high luminosity required for measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through it. Finally, the emitted Cherenkov photons are detected by a micro-channel plate multi-anode Photomultiplier Tube (MCP-PMT) and processed by fast electronics.« less

Construction of the optical part of a time-of-flight detector prototype for the AFP detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nozka, L.; Adamczyk, L.; Avoni, G.

We present the construction of the optical part of the ToF (time-of-flight) subdetector prototype for the AFP (ATLAS Forward Proton) detector. The ToF detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgrounds that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from themore » ToF allows the proton tagger to operate at the high luminosity required for measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through it. Finally, the emitted Cherenkov photons are detected by a micro-channel plate multi-anode Photomultiplier Tube (MCP-PMT) and processed by fast electronics.« less

High-resolution 3D-constructive interference in steady-state MR imaging and 3D time-of-flight MR angiography in neurovascular compression: a comparison between 3T and 1.5T.

PubMed

Garcia, M; Naraghi, R; Zumbrunn, T; Rösch, J; Hastreiter, P; Dörfler, A

2012-08-01

High-resolution MR imaging is useful for diagnosis and preoperative planning in patients with NVC. Because high-field MR imaging promises higher SNR and resolution, the aim of this study was to determine the value of high-resolution 3D-CISS and 3D-TOF MRA at 3T compared with 1.5T in patients with NVC. Forty-seven patients with NVC, trigeminal neuralgia, hemifacial spasm, and glossopharyngeal neuralgia were examined at 1.5T and 3T, including high-resolution 3D-CISS and 3D-TOF MRA sequences. Delineation of anatomic structures, overall image quality, severity of artifacts, visibility of NVC, and assessment of the SNR and CNR were compared between field strengths. SNR and CNR were significantly higher at 3T (P < .001). Significantly better anatomic conspicuity, including delineation of CNs, nerve branches, and assessment of small vessels, was obtained at 3T (P < .02). Severity of artifacts was significantly lower at 3T (P < .001). Consequently, overall image quality was significantly higher at 3T. NVC was significantly better delineated at 3T (P < .001). Six patients in whom NVC was not with certainty identifiable at 1.5T were correctly diagnosed at 3T. Patients with NVC may benefit from the higher resolution and greater sensitivity of 3T for preoperative assessment of NVC, and 3T may be of particular value when 1.5T is equivocal.

Heterologous Expression of Aspergillus niger β-d-Xylosidase (XlnD): Characterization on Lignocellulosic Substrates

NASA Astrophysics Data System (ADS)

Selig, Michael J.; Knoshaug, Eric P.; Decker, Stephen R.; Baker, John O.; Himmel, Michael E.; Adney, William S.

The gene encoding a glycosyl hydrolase family 3 xylan 1,4-beta-xylosidase, xlnD, was successfully cloned from Aspergillus niger strain ATCC 10864. The recombinant product was expressed in Aspergillus awamori, purified by column chromatography, and verified by matrix-assisted laser desorption ionization, tandem time of flight (MALDI-TOF/ TOF) mass spectroscopy of tryptic digests. The T max was determined using differential scanning microcalorimetry (DSC) to be 78.2 °C; the K m and k cat were found to be 255 μM and 13.7 s-1, respectively, using pNP-β-d-xylopyranoside as substrate. End-product inhibition by d-xylose was also verified and shown to be competitive; the K i for this inhibition was estimated to be 3.3 mM. XlnD was shown to efficiently hydrolyze small xylo-oligomers to monomeric xylose, making it a critical hydrolytic activity in cases where xylose is to be recovered from biomass conversion processes. In addition, the presence of the XlnD was shown to synergistically enhance the ability of an endoxylanase, XynA from Thermomyces lanuginosus, to convert xylan present in selected pretreated lignocellulosic substrates. Furthermore, the addition of the XynA/XlnD complex was effective in enhancing the ability of a simplified cellulase complex to convert glucan present in the substrates.

Heterologous expression of Aspergillus niger beta-D-xylosidase (XlnD): characterization on lignocellulosic substrates.

PubMed

Selig, Michael J; Knoshaug, Eric P; Decker, Stephen R; Baker, John O; Himmel, Michael E; Adney, William S

2008-03-01

The gene encoding a glycosyl hydrolase family 3 xylan 1,4-beta-xylosidase, xlnD, was successfully cloned from Aspergillus niger strain ATCC 10864. The recombinant product was expressed in Aspergillus awamori, purified by column chromatography, and verified by matrix-assisted laser desorption ionization, tandem time of flight (MALDI-TOF/TOF) mass spectroscopy of tryptic digests. The T (max) was determined using differential scanning microcalorimetry (DSC) to be 78.2 degrees C; the K (m) and k (cat) were found to be 255 microM and 13.7 s(-1), respectively, using pNP-beta-D-xylopyranoside as substrate. End-product inhibition by D-xylose was also verified and shown to be competitive; the K (i) for this inhibition was estimated to be 3.3 mM. XlnD was shown to efficiently hydrolyze small xylo-oligomers to monomeric xylose, making it a critical hydrolytic activity in cases where xylose is to be recovered from biomass conversion processes. In addition, the presence of the XlnD was shown to synergistically enhance the ability of an endoxylanase, XynA from Thermomyces lanuginosus, to convert xylan present in selected pretreated lignocellulosic substrates. Furthermore, the addition of the XynA/XlnD complex was effective in enhancing the ability of a simplified cellulase complex to convert glucan present in the substrates.

Heterologous Expression of Aspergillus Niger --beta--D-Xylosidase (XInD): Characterization on Lignocellulosic Substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Selig, M. J.; Knoshaug, E. P.; Decker, S. R.

2008-01-01

The gene encoding a glycosyl hydrolase family 3 xylan 1,4-beta-xylosidase, xlnD, was successfully cloned from Aspergillus niger strain ATCC 10864. The recombinant product was expressed in Aspergillus awamori, purified by column chromatography, and verified by matrix-assisted laser desorption ionization, tandem time of flight (MALDI-TOF/TOF) mass spectroscopy of tryptic digests. The T{sub max} was determined using differential scanning microcalorimetry (DSC) to be 78.2 C; the K{sub m} and k{sub cat} were found to be 255 {micro}M and 13.7 s{sup -1}, respectively, using {rho}NP-{Beta}-d-xylopyranoside as substrate. End-product inhibition by d-xylose was also verified and shown to be competitive; the K{sub i} formore » this inhibition was estimated to be 3.3 mM. XlnD was shown to efficiently hydrolyze small xylo-oligomers to monomeric xylose, making it a critical hydrolytic activity in cases where xylose is to be recovered from biomass conversion processes. In addition, the presence of the XlnD was shown to synergistically enhance the ability of an endoxylanase, XynA from Thermomyces lanuginosus, to convert xylan present in selected pretreated lignocellulosic substrates. Furthermore, the addition of the XynA/XlnD complex was effective in enhancing the ability of a simplified cellulase complex to convert glucan present in the substrates.« less

A Robotic Platform for Corn Seedling Morphological Traits Characterization

PubMed Central

Lu, Hang; Tang, Lie; Whitham, Steven A.; Mei, Yu

2017-01-01

Crop breeding plays an important role in modern agriculture, improving plant performance, and increasing yield. Identifying the genes that are responsible for beneficial traits greatly facilitates plant breeding efforts for increasing crop production. However, associating genes and their functions with agronomic traits requires researchers to observe, measure, record, and analyze phenotypes of large numbers of plants, a repetitive and error-prone job if performed manually. An automated seedling phenotyping system aimed at replacing manual measurement, reducing sampling time, and increasing the allowable work time is thus highly valuable. Toward this goal, we developed an automated corn seedling phenotyping platform based on a time-of-flight of light (ToF) camera and an industrial robot arm. A ToF camera is mounted on the end effector of the robot arm. The arm positions the ToF camera at different viewpoints for acquiring 3D point cloud data. A camera-to-arm transformation matrix was calculated using a hand-eye calibration procedure and applied to transfer different viewpoints into an arm-based coordinate frame. Point cloud data filters were developed to remove the noise in the background and in the merged seedling point clouds. A 3D-to-2D projection and an x-axis pixel density distribution method were used to segment the stem and leaves. Finally, separated leaves were fitted with 3D curves for morphological traits characterization. This platform was tested on a sample of 60 corn plants at their early growth stages with between two to five leaves. The error ratios of the stem height and leave length measurements are 13.7% and 13.1%, respectively, demonstrating the feasibility of this robotic system for automated corn seedling phenotyping. PMID:28895892

A Robotic Platform for Corn Seedling Morphological Traits Characterization.

PubMed

Lu, Hang; Tang, Lie; Whitham, Steven A; Mei, Yu

2017-09-12

Crop breeding plays an important role in modern agriculture, improving plant performance, and increasing yield. Identifying the genes that are responsible for beneficial traits greatly facilitates plant breeding efforts for increasing crop production. However, associating genes and their functions with agronomic traits requires researchers to observe, measure, record, and analyze phenotypes of large numbers of plants, a repetitive and error-prone job if performed manually. An automated seedling phenotyping system aimed at replacing manual measurement, reducing sampling time, and increasing the allowable work time is thus highly valuable. Toward this goal, we developed an automated corn seedling phenotyping platform based on a time-of-flight of light (ToF) camera and an industrial robot arm. A ToF camera is mounted on the end effector of the robot arm. The arm positions the ToF camera at different viewpoints for acquiring 3D point cloud data. A camera-to-arm transformation matrix was calculated using a hand-eye calibration procedure and applied to transfer different viewpoints into an arm-based coordinate frame. Point cloud data filters were developed to remove the noise in the background and in the merged seedling point clouds. A 3D-to-2D projection and an x -axis pixel density distribution method were used to segment the stem and leaves. Finally, separated leaves were fitted with 3D curves for morphological traits characterization. This platform was tested on a sample of 60 corn plants at their early growth stages with between two to five leaves. The error ratios of the stem height and leave length measurements are 13.7% and 13.1%, respectively, demonstrating the feasibility of this robotic system for automated corn seedling phenotyping.

2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jian, E-mail: lujian@ujs.edu.cn; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013; Zhou, Zhongping

Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells. - Highlights: • Colon epithelial cell linemore » is firstly successfully transformed by cadmium. • 2D-DIGE is applied to visualize the differentially expressed proteins. • RhoA plays an important role in cadmium induced malignant transformation. • Bioinformatic and experimental methods are combined to explore new mechanisms.« less

High-resolution gadolinium-enhanced 3D MRA of the infrapopliteal arteries. Lessons for improving bolus-chase peripheral MRA.

PubMed

Hood, Maureen N; Ho, Vincent B; Foo, Thomas K F; Marcos, Hani B; Hess, Sandra L; Choyke, Peter L

2002-09-01

Peripheral magnetic resonance angiography (MRA) is growing in use. However, methods of performing peripheral MRA vary widely and continue to be optimized, especially for improvement in illustration of infrapopliteal arteries. The main purpose of this project was to identify imaging factors that can improve arterial visualization in the lower leg using bolus chase peripheral MRA. Eighteen healthy adults were imaged on a 1.5T MR scanner. The calf was imaged using conventional three-station bolus chase three-dimensional (3D) MRA, two dimensional (2D) time-of-flight (TOF) MRA and single-station Gadolinium (Gd)-enhanced 3D MRA. Observer comparisons of vessel visualization, signal to noise ratios (SNR), contrast to noise ratios (CNR) and spatial resolution comparisons were performed. Arterial SNR and CNR were similar for all three techniques. However, arterial visualization was dramatically improved on dedicated, arterial-phase Gd-enhanced 3D MRA compared with the multi-station bolus chase MRA and 2D TOF MRA. This improvement was related to optimization of Gd-enhanced 3D MRA parameters (fast injection rate of 2 mL/sec, high spatial resolution imaging, the use of dedicated phased array coils, elliptical centric k-space sampling and accurate arterial phase timing for image acquisition). The visualization of the infrapopliteal arteries can be substantially improved in bolus chase peripheral MRA if voxel size, contrast delivery, and central k-space data acquisition for arterial enhancement are optimized. Improvements in peripheral MRA should be directed at these parameters.

Next generation PET data acquisition architectures

NASA Astrophysics Data System (ADS)

Jones, W. F.; Reed, J. H.; Everman, J. L.; Young, J. W.; Seese, R. D.

1997-06-01

New architectures for higher performance data acquisition in PET are proposed. Improvements are demanded primarily by three areas of advancing PET state of the art. First, larger detector arrays such as the Hammersmith ECAT/sup (R/) EXACT HR/sup ++/ exceed the addressing capacity of 32 bit coincidence event words. Second, better scintillators (LSO) make depth-of interaction (DOI) and time-of-flight (TOF) operation more practical. Third, fully optimized single photon attenuation correction requires higher rates of data collection. New technologies which enable the proposed third generation Real Time Sorter (RTS III) include: (1) 80 Mbyte/sec Fibre Channel RAID disk systems, (2) PowerPC on both VMEbus and PCI Local bus, and (3) quadruple interleaved DRAM controller designs. Data acquisition flexibility is enhanced through a wider 64 bit coincidence event word. PET methodology support includes DOI (6 bits), TOF (6 bits), multiple energy windows (6 bits), 512/spl times/512 sinogram indexes (18 bits), and 256 crystal rings (16 bits). Throughput of 10 M events/sec is expected for list-mode data collection as well as both on-line and replay histogramming. Fully efficient list-mode storage for each PET application is provided by real-time bit packing of only the active event word bits. Real-time circuits provide DOI rebinning.

Obliteration dynamics in cerebral arteriovenous malformations after cyberknife radiosurgery: quantification with sequential nidus volumetry and 3-tesla 3-dimensional time-of-flight magnetic resonance angiography.

PubMed

Wowra, Berndt; Muacevic, Alexander; Tonn, Jörg-Christian; Schoenberg, Stefan O; Reiser, Maximilian; Herrmann, Karin A

2009-02-01

To investigate the time-dependent obliteration of cerebral arteriovenous malformations (cAVM) after CyberKnife radiosurgery (CKRS) (Accuray, Inc., Sunnyvale, CA) by means of sequential 3-T, 3-dimensional (3D), time-of-flight (TOF) magnetic resonance angiography (MRA), and volumetry of the arteriovenous malformation (AVM) nidus. In this prospective study, 3D TOF MRA was performed on 20 patients with cAVMs treated by single-fraction CKRS. Three-dimensional TOF MRA was performed on a 3-T, 32-channel magnetic resonance scanner (Magnetom TIM Trio; Siemens Medical Solutions, Erlangen, Germany) with isotropic voxel size at a spatial resolution of 0.6 x 0.6 x 0.6 mm3. The time-dependent relative decay of the transnidal blood flow evidenced by 3D TOF MRA was referred to as "obliteration dynamics." Volumetry of the nidus size was performed with OsiriX imaging software (OsiriX Foundation, Geneva, Switzerland). All patients had 3 to 4 follow-up examinations at 3- to 6-month intervals over a minimum follow-up period of 9 months. Subtotal obliteration was determined if the residual nidus volume was 5% or less of the initial nidus volume. Stata/IC software (Version 10.0; Stata Corp., College Station, TX) was used for statistical analysis and to identify potential factors of AVM obliteration. Regarding their clinical status, case history, and pretreatments, the participants of this study represent difficult-to-treat cAVM patients. The median nidus volume was 1.8 mL (range, 0.4-12.5 mL); the median minimum dose prescribed to the nidus was 22 Gy (range, 16-24 Gy) delivered to the 67% isodose line (range, 55-80%). CKRS was well tolerated, with complications in 2 patients. No further hemorrhages occurred after RS, except 1 small and clinically inapparent incident. The median follow-up period after RS was 25.0 months (range, 11.7-36.8 months). After RS, a statistically significant obliteration was observed in all patients. However, the obliteration dynamics of the cAVMs showed a pronounced variability, with 2 types of post-therapeutic behavior identified. cAVMs of Group A showed a faster reduction of transnidal blood flow than cAVMs in Group B. The median time to subtotal obliteration was 23.8 months for all patients, 11.6 months for patients in Group A, and 27.8 months for patients in Group B (P = 0.05). Logistic regression analysis revealed dose homogeneity and the circumscribed isodose to be the only variables (P < 0.01) associated with the obliteration dynamics in this study. The cumulative complete angiographic obliteration rate was 67% (95% confidence interval, 32-95%) 2 years after RS. The use of sequential 3D TOF MRA at 3 T and nidus volumetry enables a noninvasive quantitative assessment of the dynamic obliteration process induced by CKRS in cAVMs. This method may be helpful to identify factors related to AVM obliteration after RS when larger patient cohorts become available.

4D flow MRI assessment of extracranial-intracranial bypass: qualitative and quantitative evaluation of the hemodynamics.

PubMed

Sekine, Tetsuro; Takagi, Ryo; Amano, Yasuo; Murai, Yasuo; Orita, Erika; Matsumura, Yoshio; Kumita, Shin-Ichiro

2016-03-01

Our aim was to assess the feasibility of using time-resolved 3D phase-contrast (4D flow) MRI to characterize extracranial-intracranial (EC-IC) bypass. We enrolled 32 patients who underwent EC-IC bypass (15 men, 17 women; mean age 66.4 years). In all, 16 underwent radial artery graft (RAG) bypass and 16 underwent superficial temporal artery (STA) bypass. 4D flow MRI, time-of-flight (TOF) magnetic resonance angiography (MRA), and computed tomography angiography (CTA) were performed. Bypass patency, flow direction, and blood flow volume (BFV) of each artery were determined by 4D flow MRI. Arterial diameters were measured by TOF-MRA and CTA. We compared RAG and STA bypasses by evaluating the flow direction and BFV of each artery. We evaluated the correlation between arterial diameters (measured by CTA or MRA) and the BFV and the detectability of flow direction (measured by 4D flow MRI) of each artery. 4D flow MRI confirmed the patency of each bypass artery. Flow direction of the M1 segment of the middle cerebral artery and BFV in the bypass artery differed between RAG and STA groups (p < 0.01). BFV in the bypass slightly correlated with the diameters on CTA (p < 0.05, R (2) = 0.287). Of the 29 arteries in the circle of Willis, nine were not depicted on 4D flow MRI. Cutoff values for arterial diameters on CTA and TOF-MRA for detecting the artery on 4D flow MRI were 2.4 and 1.8 mm, respectively. 4D flow MRI provided unique information for characterizing EC-IC bypasses, although this detectability is limited when addressing small arteries with slow flow.

Imaging thermal plasma mass and velocity analyzer

NASA Astrophysics Data System (ADS)

Yau, Andrew W.; Howarth, Andrew

2016-07-01

We present the design and principle of operation of the imaging ion mass and velocity analyzer on the Enhanced Polar Outflow Probe (e-POP), which measures low-energy (1-90 eV/e) ion mass composition (1-40 AMU/e) and velocity distributions using a hemispherical electrostatic analyzer (HEA), a time-of-flight (TOF) gate, and a pair of toroidal electrostatic deflectors (TED). The HEA and TOF gate measure the energy-per-charge and azimuth of each detected ion and the ion transit time inside the analyzer, respectively, providing the 2-D velocity distribution of each major ionospheric ion species and resolving the minor ion species under favorable conditions. The TED are in front of the TOF gate and optionally sample ions at different elevation angles up to ±60°, for measurement of 3-D velocity distribution. We present examples of observation data to illustrate the measurement capability of the analyzer, and show the occurrence of enhanced densities of heavy "minor" O++, N+, and molecular ions and intermittent, high-velocity (a few km/s) upward and downward flowing H+ ions in localized regions of the quiet time topside high-latitude ionosphere.

Ultrasonic transmission at solid-liquid interfaces

NASA Astrophysics Data System (ADS)

Wadley, Haydn N. G.; Queheillalt, Douglas T.; Lu, Yichi

1996-11-01

New non-invasive solid-liquid interface sensing technologies are a key element in the development of improved Bridman growth techniques for synthesizing single crystal semiconductor materials. Laser generated and optically detect ultrasonic techniques have the potential to satisfy this need. Using an anisotropic 3D ray tracing methodology combined with elastic constant data measured near the melting point, ultrasonic propagation in cylindrical single crystal bodies containing either a convex, flat, or concave solid-liquid interface has been simulated. Ray paths, wavefronts and the time-of-flight (TOF) of rays that travel from a source to an arbitrarily positioned receiver have all been calculated. Experimentally measured TOF data have been collected using laser generated, optically detected ultrasound on model systems with independently known interface shapes. Both numerically simulated and experimental data have shown that the solidification region can be easily identified from transmission TOF measurements because the velocity of the liquid is much smaller than that of the solid. Since convex and concave solid-liquid interfaces result in distinctively different TOF data profiles, the interface shape can also be readily determined from the TOF data. When TOF data collected in the diametral plane is used in conjunction with a nonlinear least squares algorithm, the interface geometry has been successfully reconstructed and ultrasonic velocities of both the solid and liquid obtained with reconstruction errors less than 5 percent.

Unimolecular dissociation of protonated trans-1,4-diphenyl-2-butene-1,4-dione in the gas phase: rearrangement versus simple cleavage.

PubMed

Wu, Lianming; Liu, David Q; Vogt, Frederick G

2006-01-01

Fragmentation mechanisms of trans-1,4-diphenyl-2-butene-1,4-dione were studied using a variety of mass spectrometric techniques. The major fragmentation pathways occur by various rearrangements by loss of H(2)O, CO, H(2)O and CO, and CO(2). The other fragmentation pathways via simple alpha cleavages were also observed but accounted for the minor dissociation channels in both a two-dimensional (2-D) linear ion trap and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The elimination of CO(2) (rather than CH(3)CHO or C(3)H(8)), which was confirmed by an exact mass measurement using the Q-TOF instrument, represented a major fragmentation pathway in the 2-D linear ion trap mass spectrometer. However, the elimination of H(2)O and CO becomes more competitive in the beam-type Q-TOF instrument. The loss of CO is observed in both the MS(2) experiment of m/z 237 and the MS(3) experiment of m/z 219 but via the different transition states. The data suggest that the olefinic double bond in protonated trans-1,4-diphenyl-2-butene-1,4-dione plays a key role in stabilizing the rearrangement transition states and increasing the bond dissociation (cleavage) energy to give favorable rearrangement fragmentation pathways. Copyright (c) 2006 John Wiley & Sons, Ltd.

Protein profiling as early detection biomarkers for TiO2 nanoparticle toxicity in Daphnia magna.

PubMed

Sá-Pereira, Paula; Diniz, Mário S; Moita, Liliana; Pinheiro, Teresa; Mendonça, Elsa; Paixão, Susana M; Picado, Ana

2018-05-01

The mode of action for nanoparticle (NP) toxicity in aquatic organisms is not yet fully understood. In this work, a strategy other than toxicity testing was applied to Daphnia magna exposed to TiO 2 -NPs: the use of nuclear microscopy and the assessment of protein profile. D. magna is a keystone species broadly used as a model system in ecotoxicology. Titanium (Ti) was found in the D. magna digestive tract, mainly in the gut. The penetration of Ti into the epithelial region was greater at higher exposure levels and also observed in eggs in the brood pouch. The protein profile of individuals exposed to different concentrations showed that 2.8 and 5.6 mg/L TiO 2 -NP concentrations induced an over-expression of the majority of proteins, in particular proteins with molecular weight of ∼120, 85 and 15 kDa, while 11.2 mg/L TiO 2 -NP had an inhibitory effect on protein expression. The Matrix-assisted laser desorption ionization with tandem time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis of these proteins consistently identified them as vitellogenin (Vtg)-like proteins, associated with enzymes involved in redox balance. These results indicate that Vtg-like proteins are up-regulated in D. magna exposed to TiO 2 -NPs. Vitellogenesis is associated with the reproduction system, suggesting that TiO 2 -NP exposure can impair reproduction by affecting this process. The precise mode of action of TiO 2 -NPs is still unclear and the results from this study are a first attempt to identify specific proteins as potential markers of TiO 2 -NP toxicity in D. magna, providing useful information for future research.

2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima

PubMed Central

Hayashi, Gohei; Moro, Carlo F; Rohila, Jai Singh; Shibato, Junko; Kubo, Akihiro; Imanaka, Tetsuji; Kimura, Shinzo; Ozawa, Shoji; Fukutani, Satoshi; Endo, Satoru; Ichikawa, Katsuki; Agrawal, Ganesh Kumar; Shioda, Seiji; Hori, Motohide; Fukumoto, Manabu; Rakwal, Randeep

2015-01-01

The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves. PMID:26451896

Characterization of bioactive compounds of Annona cherimola L. leaves using a combined approach based on HPLC-ESI-TOF-MS and NMR.

PubMed

Díaz-de-Cerio, Elixabet; Aguilera-Saez, Luis Manuel; Gómez-Caravaca, Ana María; Verardo, Vito; Fernández-Gutiérrez, Alberto; Fernández, Ignacio; Arráez-Román, David

2018-06-01

Annona cherimola Mill. (cherimoya) has widely been used as food crop. The leaves of this tree possess several health benefits, which are, in general, attributed mainly to its bioactive composition. However, literature concerning a comprehensive characterization based on a combined approach, which consists of nuclear magnetic resonance (NMR) and high-performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-TOF-MS), from these leaves is scarce. Thus, the aim of this work was to study the polar profile of full extracts of cherimoya leaves by using these tools. Thus, a total of 77 compounds have been characterized, 12 of which were identified by both techniques. Briefly, 23 compounds were classified as amino acids, organic acids, carbohydrates, cholines, phenolic acid derivatives, and flavonoids by NMR, while 66 metabolites were divided into sugars, amino acids, phenolic acids and derivatives, flavonoids, phenylpropanoids, and other polar compounds by HPLC-TOF-MS. It is worth mentioning that different solvent mixtures were tested and the total phenolic content in the extracts quantified (TPC via HPLC-TOF-MS). The tendency observed was EtOH/water 80/20 (v/v) (17.0 ± 0.2 mg TPC/g leaf dry weight (d.w.)) ≥ acetone/water 70/30 (v/v) (16.1 ± 0.7 mg TPC/g leaf d.w.) > EtOH/water 70/30 (v/v) (14.0 ± 0.3 mg TPC/g leaf d.w.) > acetone/water 80/20 (v/v) (13.5 ± 0.4 mg TPC/g leaf d.w.). Importantly, flavonoids derivatives were between 63 and 76% of the TPC in those extracts. Major compounds were sucrose, glucose (α and β), and proline, and chlorogenic acid and rutin for NMR and HPLC-TOF-MS, respectively. Graphical abstract The combined use of LC-HRMS and NMR is a potential synergic combination for a comprehensive metabolite composition of cherimoya leaves.

Accurate characterization of carcinogenic DNA adducts using MALDI tandem time-of-flight mass spectrometry

NASA Astrophysics Data System (ADS)

Barnes, Charles A.; Chiu, Norman H. L.

2009-01-01

Many chemical carcinogens and their in vivo activated metabolites react readily with genomic DNA, and form covalently bound carcinogen-DNA adducts. Clinically, carcinogen-DNA adducts have been linked to various cancer diseases. Among the current methods for DNA adduct analysis, mass spectroscopic method allows the direct measurement of unlabeled DNA adducts. The goal of this study is to explore the use of matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) to determine the identity of carcinogen-DNA adducts. Two of the known carcinogenic DNA adducts, namely N-(2'-deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenyl-imidazo [4,5-b] pyridine (dG-C8-PhIP) and N-(2'-deoxyguanosin-8yl)-4-aminobiphenyl (dG-C8-ABP), were selected as our models. In MALDI-TOF MS measurements, the small matrix ion and its cluster ions did not interfere with the measurements of both selected dG adducts. To achieve a higher accuracy for the characterization of selected dG adducts, 1 keV collision energy in MALDI-TOF/TOF MS/MS was used to measure the adducts. In comparison to other MS/MS techniques with lower collision energies, more extensive precursor ion dissociations were observed. The detection of the corresponding fragment ions allowed the identities of guanine, PhIP or ABP, and the position of adduction to be confirmed. Some of the fragment ions of dG-C8-PhIP have not been reported by other MS/MS techniques.

3D vision system for intelligent milking robot automation

NASA Astrophysics Data System (ADS)

Akhloufi, M. A.

2013-12-01

In a milking robot, the correct localization and positioning of milking teat cups is of very high importance. The milking robots technology has not changed since a decade and is based primarily on laser profiles for teats approximate positions estimation. This technology has reached its limit and does not allow optimal positioning of the milking cups. Also, in the presence of occlusions, the milking robot fails to milk the cow. These problems, have economic consequences for producers and animal health (e.g. development of mastitis). To overcome the limitations of current robots, we have developed a new system based on 3D vision, capable of efficiently positioning the milking cups. A prototype of an intelligent robot system based on 3D vision for real-time positioning of a milking robot has been built and tested under various conditions on a synthetic udder model (in static and moving scenarios). Experimental tests, were performed using 3D Time-Of-Flight (TOF) and RGBD cameras. The proposed algorithms permit the online segmentation of teats by combing 2D and 3D visual information. The obtained results permit the teat 3D position computation. This information is then sent to the milking robot for teat cups positioning. The vision system has a real-time performance and monitors the optimal positioning of the cups even in the presence of motion. The obtained results, with both TOF and RGBD cameras, show the good performance of the proposed system. The best performance was obtained with RGBD cameras. This latter technology will be used in future real life experimental tests.

Cerebral Perforating Artery Disease : Characteristics on High-Resolution Magnetic Resonance Imaging.

PubMed

Liang, Jianye; Liu, Yiyong; Xu, Xiaoshuang; Shi, Changzheng; Luo, Liangping

2018-03-23

Our aims were to evaluate the feasibility of high-resolution magnetic resonance imaging (HR-MRI) for displaying the cerebral perforating arteries in normal subjects and to discuss the value of HR-MRI for detecting the causes of infarctions in the territory of the lenticulostriate artery (LSA). Included in this study were 31 healthy subjects and 28 patients who had infarctions in the territory supplied by the LSA. The T1-weighted imaging (T1WI), T2WI, diffusion-weighted imaging (DWI), and HR-MRI, including 3‑dimensional time-of-flight magnetic resonance angiography (3D-TOF-MRA) and 3D fast spin-echo T1WI (namely CUBE T1 in GE Healthcare), were applied on a 3-Tesla scanner. The numbers and route of the perforating arteries on both sides were independently confirmed on HR-MRI by two physicians. The Wilcoxon test was used to compare the differences. The numbers of perforating arteries in healthy subjects observed on 3D-TOF-MRA were as follows: numbers of the bilateral recurrent artery of Heubner (RAH) ranged from 0-3 (median 1), numbers of the left LSA ranged from 0-7 (median 3), numbers of the right LSA ranged from 0-5 (median 3), numbers of the bilateral anterior choroidal artery ranged from 1-2 (median 1) and the numbers of the bilateral thalamoperforating artery ranged from 1-2 (median 1). In the patients with lenticulostriate infarctions, the numbers of LSAs on the affected side were lower than on the opposite and ipsilateral sides in the healthy subjects. The results were statistically significant. An abnormality of the RAH may lead to a centrum semiovale infarct pattern, whereas an abnormality of the LSA is associated with a corona radiata infarct pattern. The use of HR 3D-TOF-MRA and CUBE T1 had unique advantages in displaying the tiny perforating arteries in vivo. Moreover, effective recognition of the associated cerebral perforating artery and infarct patterns may enhance our understanding of the mechanism of stroke in patients with lenticulostriate infarctions.

No scanning depth imaging system based on TOF

NASA Astrophysics Data System (ADS)

Sun, Rongchun; Piao, Yan; Wang, Yu; Liu, Shuo

2016-03-01

To quickly obtain a 3D model of real world objects, multi-point ranging is very important. However, the traditional measuring method usually adopts the principle of point by point or line by line measurement, which is too slow and of poor efficiency. In the paper, a no scanning depth imaging system based on TOF (time of flight) was proposed. The system is composed of light source circuit, special infrared image sensor module, processor and controller of image data, data cache circuit, communication circuit, and so on. According to the working principle of the TOF measurement, image sequence was collected by the high-speed CMOS sensor, and the distance information was obtained by identifying phase difference, and the amplitude image was also calculated. Experiments were conducted and the experimental results show that the depth imaging system can achieve no scanning depth imaging function with good performance.

Identification of prohibitin 1 as a potential prognostic biomarker in human pancreatic carcinoma using modified aqueous two-phase partition system combined with 2D-MALDI-TOF-TOF-MS/MS.

PubMed

Zhong, Ning; Cui, Yazhou; Zhou, Xiaoyan; Li, Tianliang; Han, Jinxiang

2015-02-01

Membrane proteins are an important source of potential targets for anticancer drugs or biomarkers for early diagnosis. In this study, we used a modified aqueous two-phase partition system combined with two-dimensional (2D) matrix-assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS, 2D-MALDI-TOF-TOF-MS/MS) analysis to isolate and identify membrane proteins in PANC-1 pancreatic cancer cells. Using this method, we identified 55 proteins, of which 31 (56.4 %) were membrane proteins, which, according to gene ontology annotation, are associated with various cellular processes including cell signal transduction, differentiation, and apoptosis. Immunohistochemical analysis showed that the expression level of one of the identified mitochondria membrane proteins, prohibitin 1 (PHB1), is correlated with pancreatic carcinoma differentiation; PHB1 is expressed at a higher level in normal pancreatic tissue than in well-differentiated carcinoma tissue. Further studies showed that PHB1 plays a proapoptotic role in human pancreatic cancer cells, which suggests that PHB1 has antitumorigenic properties. In conclusion, we have provided a modified method for isolating and identifying membrane proteins and demonstrated that PHB1 may be a promising biomarker for early diagnosis and therapy of pancreatic (and potentially other) cancers.

Compton scatter tomography in TOF-PET

NASA Astrophysics Data System (ADS)

Hemmati, Hamidreza; Kamali-Asl, Alireza; Ay, Mohammadreza; Ghafarian, Pardis

2017-10-01

Scatter coincidences contain hidden information about the activity distribution on the positron emission tomography (PET) imaging system. However, in conventional reconstruction, the scattered data cause the blurring of images and thus are estimated and subtracted from detected coincidences. List mode format provides a new aspect to use time of flight (TOF) and energy information of each coincidence in the reconstruction process. In this study, a novel approach is proposed to reconstruct activity distribution using the scattered data in the PET system. For each single scattering coincidence, a scattering angle can be determined by the recorded energy of the detected photons, and then possible locations of scattering can be calculated based on the scattering angle. Geometry equations show that these sites lie on two arcs in 2D mode or the surface of a prolate spheroid in 3D mode, passing through the pair of detector elements. The proposed method uses a novel and flexible technique to estimate source origin locations from the possible scattering locations, using the TOF information. Evaluations were based on a Monte-Carlo simulation of uniform and non-uniform phantoms at different resolutions of time and detector energy. The results show that although the energy uncertainties deteriorate the image spatial resolution in the proposed method, the time resolution has more impact on image quality than the energy resolution. With progress of the TOF system, the reconstruction using the scattered data can be used in a complementary manner, or to improve image quality in the next generation of PET systems.

Neutron spectroscopy for pulsed beams with frame overlap using a double time-of-flight technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrig, K. P.; Goldblum, B. L.; Brown, J. A.

A new double time-of- ight (dTOF) neutron spectroscopy technique has been developed for pulsed broad spectrum sources with a duty cycle that results in frame overlap, where fast neutrons from a given pulse overtake slower neutrons from previous pulses. Using a tunable beam at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory, neutrons were produced via thick-target breakup of 16 MeV deuterons on a beryllium target in the cyclotron vault. The breakup spectral shape was deduced from a dTOF measurement using an array of EJ-309 organic liquid scintillators. Simulation of the neutron detection efficiency of the scintillator array was performedmore » using both GEANT4 and MCNP6. The efficiency- corrected spectral shape was normalized using a foil activation technique to obtain the energy-dependent flux of the neutron beam at zero degrees with respect to the incoming deuteron beam. The dTOF neutron spectrum was compared to spectra obtained using HEPROW and GRAVEL pulse height spectrum unfolding techniques. While the unfolding and dTOF results exhibit some discrepancies in shape, the integrated flux values agree within two standard deviations. As a result, this method obviates neutron time-of-flight spectroscopy challenges posed by pulsed beams« less

Neutron Spectroscopy for pulsed beams with frame overlap using a double time-of-flight technique

NASA Astrophysics Data System (ADS)

Harrig, K. P.; Goldblum, B. L.; Brown, J. A.; Bleuel, D. L.; Bernstein, L. A.; Bevins, J.; Harasty, M.; Laplace, T. A.; Matthews, E. F.

2018-01-01

A new double time-of-flight (dTOF) neutron spectroscopy technique has been developed for pulsed broad spectrum sources with a duty cycle that results in frame overlap, where fast neutrons from a given pulse overtake slower neutrons from previous pulses. Using a tunable beam at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory, neutrons were produced via thick-target breakup of 16 MeV deuterons on a beryllium target in the cyclotron vault. The breakup spectral shape was deduced from a dTOF measurement using an array of EJ-309 organic liquid scintillators. Simulation of the neutron detection efficiency of the scintillator array was performed using both GEANT4 and MCNP6. The efficiency-corrected spectral shape was normalized using a foil activation technique to obtain the energy-dependent flux of the neutron beam at zero degrees with respect to the incoming deuteron beam. The dTOF neutron spectrum was compared to spectra obtained using HEPROW and GRAVEL pulse height spectrum unfolding techniques. While the unfolding and dTOF results exhibit some discrepancies in shape, the integrated flux values agree within two standard deviations. This method obviates neutron time-of-flight spectroscopy challenges posed by pulsed beams with frame overlap and opens new opportunities for pulsed white neutron source facilities.

Neutron spectroscopy for pulsed beams with frame overlap using a double time-of-flight technique

DOE PAGES

Harrig, K. P.; Goldblum, B. L.; Brown, J. A.; ...

2017-10-16

A new double time-of- ight (dTOF) neutron spectroscopy technique has been developed for pulsed broad spectrum sources with a duty cycle that results in frame overlap, where fast neutrons from a given pulse overtake slower neutrons from previous pulses. Using a tunable beam at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory, neutrons were produced via thick-target breakup of 16 MeV deuterons on a beryllium target in the cyclotron vault. The breakup spectral shape was deduced from a dTOF measurement using an array of EJ-309 organic liquid scintillators. Simulation of the neutron detection efficiency of the scintillator array was performedmore » using both GEANT4 and MCNP6. The efficiency- corrected spectral shape was normalized using a foil activation technique to obtain the energy-dependent flux of the neutron beam at zero degrees with respect to the incoming deuteron beam. The dTOF neutron spectrum was compared to spectra obtained using HEPROW and GRAVEL pulse height spectrum unfolding techniques. While the unfolding and dTOF results exhibit some discrepancies in shape, the integrated flux values agree within two standard deviations. As a result, this method obviates neutron time-of-flight spectroscopy challenges posed by pulsed beams« less

Can 3D light localization be reached in ‘white paint’?

NASA Astrophysics Data System (ADS)

Sperling, T.; Schertel, L.; Ackermann, M.; Aubry, G. J.; Aegerter, C. M.; Maret, G.

2016-01-01

When waves scatter multiple times in 3D random media, a disorder driven phase transition from diffusion to localization may occur (Anderson 1958 Phys. Rev. 109 1492-505 Abrahams et al 1979 Phys. Rev. Lett. 42 673-6). In ‘The question of classical localization: a theory of white paint?’ Anderson suggested the possibility to observe light localization in TiO2 samples (Anderson 1985 Phil. Mag. B 52 505-9). We recently claimed the observation of localization effects measuring photon time of flight (ToF) distributions (Störzer et al 2006 Phys. Rev. Lett. 96 063904) and evaluating transmission profiles (TPs) (Sperling et al 2013 Nat. Photonics 7 48-52) in such TiO2 samples. Here we present a careful study of the long time tail of ToF distributions and the long time behavior of the TP width for very thin samples and different turbidities that questions the localization interpretation. We further show new data that allow an alternative consistent explanation of these previous data by a fluorescence process. An adapted diffusion model including an appropriate exponential fluorescence decay accounts for the shape of the ToF distributions and the TP width. These observations question whether the strong localization regime can be reached with visible light scattering in polydisperse TiO2 samples, since the disorder parameter can hardly be increased any further in such a ‘white paint’ material.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desai, M. I.; McComas, D. J.; Allegrini, F.

We have developed a novel concept for a Compact Dual Ion Composition Experiment (CoDICE) that simultaneously provides high quality plasma and energetic ion composition measurements over 6 decades in ion energy in a wide variety of space plasma environments. CoDICE measures the two critical ion populations in space plasmas: (1) mass and ionic charge state composition and 3D velocity and angular distributions of ∼10 eV/q–40 keV/q plasma ions—CoDICE-Lo and (2) mass composition, energy spectra, and angular distributions of ∼30 keV–10 MeV energetic ions—CoDICE-Hi. CoDICE uses a common, integrated Time-of-Flight (TOF) versus residual energy (E) subsystem for measuring the two distinctmore » ion populations. This paper describes the CoDICE design concept, and presents results of the laboratory tests of the TOF portion of the TOF vs. E subsystem, focusing specifically on (1) investigation of spill-over and contamination rates on the start and stop microchannel plate (MCP) anodes vs. secondary electron steering and focusing voltages, scanned around their corresponding model-optimized values, (2) TOF measurements and resolution and angular resolution, and (3) cross-contamination of the start and stop MCPs’ singles rates from CoDICE-Lo and -Hi, and (4) energy resolution of avalanche photodiodes near the lower end of the CoDICE-Lo energy range. We also discuss physical effects that could impact the performance of the TOF vs. E subsystem in a flight instrument. Finally, we discuss advantages of the CoDICE design concept by comparing with capabilities and resources of existing flight instruments.« less

Characterizing Scintillator Response with Neutron Time-of-Flight

NASA Astrophysics Data System (ADS)

Palmisano, Kevin; Visca, Hannah; Caves, Louis; Wilkinson, Corey; McClow, Hannah; Padalino, Stephen; Forrest, Chad; Katz, Joe; Sangster, Craig; Regan, Sean

2017-10-01

Neutron scintillator diagnostics for ICF can be characterized using the neutron time-of-flight (nTOF) line on Geneseo's 1.7 MV Tandem Pelletron Accelerator. Neutron signals can be differentiated from gamma signals by employing a coincidence method called the associated particle technique (APT). In this measurement, a 2.1 MeV beam of deuterons incident on a deuterated polyethylene target produces neutrons via the d(d,n)3He reaction. A BC-412 plastic scintillator, placed at a scattering angle of 152º, detects 1.76 MeV neutrons in coincidence with the 2.56 MeV 3He ions at an associated angle of 10º. The APT is used to identify the 1.76 MeV neutron while the nTOF line determines its energy. By gating only mono-energetic neutrons, the instrument response function of the scintillator can be determined free from background scattered neutrons and gamma rays. Funded in part by a Grant from the DOE, through the Laboratory for Laser Energetics.

Increasing biomass carbon stocks in trees outside forests in China over the last three decades

NASA Astrophysics Data System (ADS)

Guo, Z. D.; Hu, H. F.; Pan, Y. D.; Birdsey, R. A.; Fang, J. Y.

2014-08-01

Trees outside forests (TOF) play important roles in national economies, ecosystem services, and international efforts for mitigating climate warming. Detailed assessment of the dynamics of carbon (C) stocks in China's TOF is necessary for fully evaluating the role of the country's trees in the national C cycle. This study is the first to explore the changes in biomass C stocks of China's TOF over the last three decades, using the national forest inventory data in six periods from 1977 to 2008. According to the definition of the forest inventory, China's TOF could be categorized into three groups: woodlands, shrubberies, and trees on non-forest land (including four-side greening trees, defined in the article, and scattered trees). We estimated biomass C stocks of woodlands and trees on non-forest land by using the provincial biomass-volume conversion equations derived from the data of low-canopy forests, and estimated the biomass C stocks of shrubberies using the provincial mean biomass density. Total TOF biomass C stock increased by 62.7% from 823 Tg C (1 Tg = 1012 g) in the initial period of 1977-1981 to 1339 Tg C in the last period of 2004-2008. As a result, China's TOF have accumulated biomass C of 516 Tg during the study period, with 12, 270, and 234 Tg in woodlands, shrubberies, and trees on non-forest land, respectively. The annual biomass C sink of China's TOF averaged 19.1 Tg C yr-1, offsetting 2.1% of the contemporary fossil-fuel CO2 emissions in the country. These estimates are equal to 16.5-20.7% of the contemporary total forest biomass C stock and 27.2% of the total forest biomass C sink in the country, suggesting that TOF are substantial components in China's tree C budget.

Time of flight emission spectroscopy of laser produced nickel plasma: Short-pulse and ultrafast excitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smijesh, N.; Chandrasekharan, K.; Joshi, Jagdish C.

2014-07-07

We report the experimental investigation and comparison of the temporal features of short-pulse (7 ns) and ultrafast (100 fs) laser produced plasmas generated from a solid nickel target, expanding into a nitrogen background. When the ambient pressure is varied in a large range of 10⁻⁶Torr to 10²Torr, the plume intensity is found to increase rapidly as the pressure crosses 1 Torr. Time of flight (TOF) spectroscopy of emission from neutral nickel (Ni I) at 361.9 nm (3d⁹(²D) 4p → 3d⁹(²D) 4s transition) reveals two peaks (fast and slow species) in short-pulse excitation and a single peak in ultrafast excitation. Themore » fast and slow peaks represent recombined neutrals and un-ionized neutrals, respectively. TOF emission from singly ionized nickel (Ni II) studied using the 428.5 nm (3p⁶3d⁸(³P) 4s→ 3p⁶3d⁹ 4s) transition shows only a single peak for either excitation. Velocities of the neutral and ionic species are determined from TOF measurements carried out at different positions (i.e., at distances of 2 mm and 4 mm, respectively, from the target surface) on the plume axis. Measured velocities indicate acceleration of neutrals and ions, which is caused by the Coulomb pull of the electrons enveloping the plume front in the case of ultrafast excitation. Both Coulomb pull and laser-plasma interaction contribute to the acceleration in the case of short-pulse excitation. These investigations provide new information on the pressure dependent temporal behavior of nickel plasmas produced by short-pulse and ultrafast laser pulses, which have potential uses in applications such as pulsed laser deposition and laser-induced nanoparticle generation.« less

Structural and fluorescence properties of the 2,2‧-methylenediphenoxy and 1,1‧-methylenedi-2-naphthoxy cyclotriphosphazene derivatives

NASA Astrophysics Data System (ADS)

Yenilmez Çiftçi, Gönül; Eker, Yakup; Şenkuytu, Elif; Yuksel, Fatma

2016-08-01

In the present work, the partially or fully substituted spiro-, ansa, open-chain forms of 2,2'-methylenediphenoxy, 1,1'-methylenedi-2-naphthoxy cyclotriphosphazene derivatives and their spectral properties were reported. The reactions of hexachlorocyclotriphosphazene [trimer, N3P3Cl6, (1)] with 2,2'-methylenediphenol (2) and 1,1'-methylenedi-2-naphthol (3) in THF produced new cyclotriphosphazene compounds (4-11). All these compounds (4-11) were fully characterized by elemental analysis, FT-IR, MALDI-TOF mass spectrometry, UV Vis, 1H, 13C and 31P NMR spectroscopy. The molecular structures of 4, 5, 7, 9 and 10 were also determined by X-ray crystallography. All five structures were found in monoclinic system, C2/c, P21/n or P21/c space groups. The fluorescence behaviour of the studied cyclotriphosphazene derivatives (9-11) were also examined in THF solution. Compound 11 showed the highest fluorescence emission behaviour that of compounds 4-10.

Lanthanum halide scintillators for time-of-flight 3-D pet

DOEpatents

Karp, Joel S [Glenside, PA; Surti, Suleman [Philadelphia, PA

2008-06-03

A Lanthanum Halide scintillator (for example LaCl.sub.3 and LaBr.sub.3) with fast decay time and good timing resolution, as well as high light output and good energy resolution, is used in the design of a PET scanner. The PET scanner includes a cavity for accepting a patient and a plurality of PET detector modules arranged in an approximately cylindrical configuration about the cavity. Each PET detector includes a Lanthanum Halide scintillator having a plurality of Lanthanum Halide crystals, a light guide, and a plurality of photomultiplier tubes arranged respectively peripherally around the cavity. The good timing resolution enables a time-of-flight (TOF) PET scanner to be developed that exhibits a reduction in noise propagation during image reconstruction and a gain in the signal-to-noise ratio. Such a PET scanner includes a time stamp circuit that records the time of receipt of gamma rays by respective PET detectors and provides timing data outputs that are provided to a processor that, in turn, calculates time-of-flight (TOF) of gamma rays through a patient in the cavity and uses the TOF of gamma rays in the reconstruction of images of the patient.

Identification of potential genetic components involved in the deviant quorum-sensing signaling pathways of Burkholderia glumae through a functional genomics approach

PubMed Central

Chen, Ruoxi; Barphagha, Inderjit K.; Ham, Jong Hyun

2015-01-01

Burkholderia glumae is the chief causal agent for bacterial panicle blight of rice. The acyl-homoserine lactone (AHL)-mediated quorum-sensing (QS) system dependent on a pair of luxI and luxR homologs, tofI and tofR, is the primary cell-to-cell signaling mechanism determining the virulence of this bacterium. Production of toxoflavin, a major virulence factor of B. glumae, is known to be dependent on the tofI/tofR QS system. In our previous study, however, it was observed that B. glumae mutants defective in tofI or tofR produced toxoflavin if they grew on the surface of a solid medium, suggesting that alternative signaling pathways independent of tofI or tofR are activated in that growth condition for the production of toxoflavin. In this study, potential genetic components involved in the tofI- and tofR-independent signaling pathways for toxoflavin production were sought through screening random mini-Tn5 mutants of B. glumae to better understand the intercellular signaling pathways of this pathogen. Fifteen and three genes were initially identified as the potential genetic elements of the tofI- and tofR-independent pathways, respectively. Especially, the ORF (bglu_2g06320) divergently transcribed from toxJ, which encodes an orphan LuxR protein and controls toxoflavin biosynthesis, was newly identified in this study as a gene required for the tofR-independent toxoflavin production and named as toxK. Among those genes, flhD, dgcB, and wzyB were further studied to validate their functions in the tofI-independent toxoflavin production, and similar studies were also conducted with qsmR and toxK for their functions in the tofR-independent toxoflavin production. This work provides a foundation for future comprehensive studies of the intercellular signaling systems of B. glumae and other related pathogenic bacteria. PMID:25806356

TOF-SIMS for Rapid Nuclear Forensics Evaluation of Uranium Oxide Particles

DTIC Science & Technology

2011-03-01

Fraction U-238 nU U metal CRM 112-A NBL Metal Assay and Isotopic .000052458 .0072017 --- .9927458 nUO2 UO2 --- NBL Commercial material...0 .992745 dU U metal CRM 115 NBL Uranium Assay .0000076 .0020291 .0000322 .9979311 dUO2 UO2 --- IBI Labs Commercial material --- .002- .0035...U500* U3O8 CRM U500 NBL Isotopic .005181 .49696 .000755 .49711 U900* U3O8 CRM U900 NBL Isotopic .007777 .90196 .003327 .08693 *Sample

Non-contrast 3D time-of-flight magnetic resonance angiography for visualization of intracranial aneurysms in patients with absolute contraindications to CT or MRI contrast.

PubMed

Yanamadala, Vijay; Sheth, Sameer A; Walcott, Brian P; Buchbinder, Bradley R; Buckley, Deidre; Ogilvy, Christopher S

2013-08-01

The preoperative evaluation of patients with intracranial aneurysms typically includes a contrast-enhanced vascular study, such as computed tomography angiography (CTA), magnetic resonance angiography (MRA), or digital subtraction angiography. However, there are numerous absolute and relative contraindications to the administration of imaging contrast agents, including pregnancy, severe contrast allergy, and renal insufficiency. Evaluation of patients with contrast contraindications thus presents a unique challenge. We identified three patients with absolute contrast contraindications who presented with intracranial aneurysms. One patient was pregnant, while the other two had previous severe anaphylactic reactions to iodinated contrast. Because of these contraindications to intravenous contrast, we performed non-contrast time-of-flight MRA with 3D reconstruction (TOF MRA with 3DR) with maximum intensity projections and volume renderings as part of the preoperative evaluation prior to successful open surgical clipping of the aneurysms. In the case of one paraclinoid aneurysm, a high-resolution non-contrast CT scan was also performed to assess the relationship of the aneurysm to the anterior clinoid process. TOF MRA with 3DR successfully identified the intracranial aneurysms and adequately depicted the surrounding microanatomy. Intraoperative findings were as predicted by the preoperative imaging studies. The aneurysms were successfully clip-obliterated, and the patients had uneventful post-operative courses. These cases demonstrate that non-contrast imaging is a viable modality to assess intracranial aneurysms as part of the surgical planning process in patients with contrast contraindications. TOF MRA with 3DR, in conjunction with high-resolution non-contrast CT when indicated, provides adequate visualization of the microanatomy of the aneurysm and surrounding structures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Impact of time-of-flight PET on quantification errors in MR imaging-based attenuation correction.

PubMed

Mehranian, Abolfazl; Zaidi, Habib

2015-04-01

Time-of-flight (TOF) PET/MR imaging is an emerging imaging technology with great capabilities offered by TOF to improve image quality and lesion detectability. We assessed, for the first time, the impact of TOF image reconstruction on PET quantification errors induced by MR imaging-based attenuation correction (MRAC) using simulation and clinical PET/CT studies. Standard 4-class attenuation maps were derived by segmentation of CT images of 27 patients undergoing PET/CT examinations into background air, lung, soft-tissue, and fat tissue classes, followed by the assignment of predefined attenuation coefficients to each class. For each patient, 4 PET images were reconstructed: non-TOF and TOF both corrected for attenuation using reference CT-based attenuation correction and the resulting 4-class MRAC maps. The relative errors between non-TOF and TOF MRAC reconstructions were compared with their reference CT-based attenuation correction reconstructions. The bias was locally and globally evaluated using volumes of interest (VOIs) defined on lesions and normal tissues and CT-derived tissue classes containing all voxels in a given tissue, respectively. The impact of TOF on reducing the errors induced by metal-susceptibility and respiratory-phase mismatch artifacts was also evaluated using clinical and simulation studies. Our results show that TOF PET can remarkably reduce attenuation correction artifacts and quantification errors in the lungs and bone tissues. Using classwise analysis, it was found that the non-TOF MRAC method results in an error of -3.4% ± 11.5% in the lungs and -21.8% ± 2.9% in bones, whereas its TOF counterpart reduced the errors to -2.9% ± 7.1% and -15.3% ± 2.3%, respectively. The VOI-based analysis revealed that the non-TOF and TOF methods resulted in an average overestimation of 7.5% and 3.9% in or near lung lesions (n = 23) and underestimation of less than 5% for soft tissue and in or near bone lesions (n = 91). Simulation results showed that as TOF resolution improves, artifacts and quantification errors are substantially reduced. TOF PET substantially reduces artifacts and improves significantly the quantitative accuracy of standard MRAC methods. Therefore, MRAC should be less of a concern on future TOF PET/MR scanners with improved timing resolution. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Simultaneous reconstruction of the activity image and registration of the CT image in TOF-PET

NASA Astrophysics Data System (ADS)

Rezaei, Ahmadreza; Michel, Christian; Casey, Michael E.; Nuyts, Johan

2016-02-01

Previously, maximum-likelihood methods have been proposed to jointly estimate the activity image and the attenuation image or the attenuation sinogram from time-of-flight (TOF) positron emission tomography (PET) data. In this contribution, we propose a method that addresses the possible alignment problem of the TOF-PET emission data and the computed tomography (CT) attenuation data, by combining reconstruction and registration. The method, called MLRR, iteratively reconstructs the activity image while registering the available CT-based attenuation image, so that the pair of activity and attenuation images maximise the likelihood of the TOF emission sinogram. The algorithm is slow to converge, but some acceleration could be achieved by using Nesterov’s momentum method and by applying a multi-resolution scheme for the non-rigid displacement estimation. The latter also helps to avoid local optima, although convergence to the global optimum cannot be guaranteed. The results are evaluated on 2D and 3D simulations as well as a respiratory gated clinical scan. Our experiments indicate that the proposed method is able to correct for possible misalignment of the CT-based attenuation image, and is therefore a very promising approach to suppressing attenuation artefacts in clinical PET/CT. When applied to respiratory gated data of a patient scan, it produced deformations that are compatible with breathing motion and which reduced the well known attenuation artefact near the dome of the liver. Since the method makes use of the energy-converted CT attenuation image, the scale problem of joint reconstruction is automatically solved.

CYP2D6 polymorphisms as predictors of outcome in breast cancer patients treated with tamoxifen: expanded polymorphism coverage improves risk stratification.

PubMed

Schroth, Werner; Hamann, Ute; Fasching, Peter A; Dauser, Silke; Winter, Stefan; Eichelbaum, Michel; Schwab, Matthias; Brauch, Hiltrud

2010-09-01

This study aimed to validate matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)/Taqman copy number assay (CNA) CYP2D6 genotyping by AmpliChip CYP450 Test for the prediction of tamoxifen metabolizer phenotypes in breast cancer, and to investigate the influence of CYP2D6 variant coverage on genotype-phenotype relationships and tamoxifen outcome. Hormone receptor-positive postmenopausal breast cancer patients (n = 492) treated with adjuvant tamoxifen, previously analyzed by MALDI-TOF MS/CNA, were reanalyzed by AmpliChip CYP450 Test and validated by independent methods. Cox proportional hazard ratios (HR) were calculated for recurrence of poor (PM) relative to extensive metabolizer (EM) phenotypes with increasing numbers of CYP2D6 variants. Kaplan-Meier distributions were calculated for different phenotype classifications. Concordance was 99.2% to 99.5% for CNA and 99.8% to 100% per CYP2D6 allele (*3, *4, *5, *9, *10, and *41). The prevalence of predicted phenotypes was 1.2% for ultrarapid metabolizer (UM), 37.2% for EM without variant, 43.5% for heterozygous EM, 9.7% for intermediate metabolizer (IM), and 8.3% for PM. Approximately, one third of patients were misclassified based on a *4 analysis only, but inclusion of all reduced-function alleles increased the PM-associated HR from 1.33 (P = 0.58) to 2.87 (P = 0.006). Kaplan-Meier analyses showed highest and lowest clinical benefit for UM and PM with respect to both the AmpliChip-based and a redefined phenotype assignment. The latter revealed significant allele-dose-dependent associations (P = 0.011) and largest effect size (HR(PM_EM) = 2.77; 95% confidence interval, 1.31-5.89). MALDI-TOF MS/CNA is suitable for accurate CYP2D6 genotyping. For tamoxifen pharmacogenetics, broad CYP2D6 allele coverage is recommended to reduce phenotype misclassification. Classification based on refined EM and reduced-function metabolizers is advisable. AACR.

Visualization of lenticulostriate arteries at 3T: Optimization of slice-selective off-resonance sinc pulse-prepared TOF-MRA and its comparison with flow-sensitive black-blood MRA.

PubMed

Okuchi, Sachi; Okada, Tomohisa; Fujimoto, Koji; Fushimi, Yasutaka; Kido, Aki; Yamamoto, Akira; Kanagaki, Mitsunori; Dodo, Toshiki; Mehemed, Taha M; Miyazaki, Mitsue; Zhou, Xiangzhi; Togashi, Kaori

2014-06-01

To optimize visualization of lenticulostriate artery (LSA) by time-of-flight (TOF) magnetic resonance angiography (MRA) with slice-selective off-resonance sinc (SORS) saturation transfer contrast pulses and to compare capability of optimal TOF-MRA and flow-sensitive black-blood (FSBB) MRA to visualize the LSA at 3T. This study was approved by the local ethics committee, and written informed consent was obtained from all the subjects. TOF-MRA was optimized in 20 subjects by comparing SORS pulses of different flip angles: 0, 400°, and 750°. Numbers of LSAs were counted. The optimal TOF-MRA was compared to FSBB-MRA in 21 subjects. Images were evaluated by the numbers and length of visualized LSAs. LSAs were significantly more visualized in TOF-MRA with SORS pulses of 400° than others (P < .003). When the optimal TOF-MRA was compared to FSBB-MRA, the visualization of LSA using FSBB (mean branch numbers 11.1, 95% confidence interval (CI) 10.0-12.1; mean total length 236 mm, 95% CI 210-263 mm) was significantly better than using TOF (4.7, 95% CI 4.1-5.3; 78 mm, 95% CI 67-89 mm) for both numbers and length of the LSA (P < .0001). LSA visualization was best with 400° SORS pulses for TOF-MRA but FSBB-MRA was better than TOF-MRA, which indicates its clinical potential to investigate the LSA on a 3T magnetic resonance imaging. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

An integrated time-of-flight versus residual energy subsystem for a compact dual ion composition experiment for space plasmas

NASA Astrophysics Data System (ADS)

Desai, M. I.; Ogasawara, K.; Ebert, R. W.; McComas, D. J.; Allegrini, F.; Weidner, S. E.; Alexander, N.; Livi, S. A.

2015-05-01

We have developed a novel concept for a Compact Dual Ion Composition Experiment (CoDICE) that simultaneously provides high quality plasma and energetic ion composition measurements over 6 decades in ion energy in a wide variety of space plasma environments. CoDICE measures the two critical ion populations in space plasmas: (1) mass and ionic charge state composition and 3D velocity and angular distributions of ˜10 eV/q-40 keV/q plasma ions—CoDICE-Lo and (2) mass composition, energy spectra, and angular distributions of ˜30 keV-10 MeV energetic ions—CoDICE-Hi. CoDICE uses a common, integrated Time-of-Flight (TOF) versus residual energy (E) subsystem for measuring the two distinct ion populations. This paper describes the CoDICE design concept, and presents results of the laboratory tests of the TOF portion of the TOF vs. E subsystem, focusing specifically on (1) investigation of spill-over and contamination rates on the start and stop microchannel plate (MCP) anodes vs. secondary electron steering and focusing voltages, scanned around their corresponding model-optimized values, (2) TOF measurements and resolution and angular resolution, and (3) cross-contamination of the start and stop MCPs' singles rates from CoDICE-Lo and -Hi, and (4) energy resolution of avalanche photodiodes near the lower end of the CoDICE-Lo energy range. We also discuss physical effects that could impact the performance of the TOF vs. E subsystem in a flight instrument. Finally, we discuss advantages of the CoDICE design concept by comparing with capabilities and resources of existing flight instruments.

An integrated time-of-flight versus residual energy subsystem for a compact dual ion composition experiment for space plasmas.

PubMed

Desai, M I; Ogasawara, K; Ebert, R W; McComas, D J; Allegrini, F; Weidner, S E; Alexander, N; Livi, S A

2015-05-01

We have developed a novel concept for a Compact Dual Ion Composition Experiment (CoDICE) that simultaneously provides high quality plasma and energetic ion composition measurements over 6 decades in ion energy in a wide variety of space plasma environments. CoDICE measures the two critical ion populations in space plasmas: (1) mass and ionic charge state composition and 3D velocity and angular distributions of ∼10 eV/q-40 keV/q plasma ions—CoDICE-Lo and (2) mass composition, energy spectra, and angular distributions of ∼30 keV-10 MeV energetic ions—CoDICE-Hi. CoDICE uses a common, integrated Time-of-Flight (TOF) versus residual energy (E) subsystem for measuring the two distinct ion populations. This paper describes the CoDICE design concept, and presents results of the laboratory tests of the TOF portion of the TOF vs. E subsystem, focusing specifically on (1) investigation of spill-over and contamination rates on the start and stop microchannel plate (MCP) anodes vs. secondary electron steering and focusing voltages, scanned around their corresponding model-optimized values, (2) TOF measurements and resolution and angular resolution, and (3) cross-contamination of the start and stop MCPs' singles rates from CoDICE-Lo and -Hi, and (4) energy resolution of avalanche photodiodes near the lower end of the CoDICE-Lo energy range. We also discuss physical effects that could impact the performance of the TOF vs. E subsystem in a flight instrument. Finally, we discuss advantages of the CoDICE design concept by comparing with capabilities and resources of existing flight instruments.

The influence of computational strategy on prediction of mechanical stress in carotid atherosclerotic plaques: comparison of 2D structure-only, 3D structure-only, one-way and fully coupled fluid-structure interaction analyses.

PubMed

Huang, Yuan; Teng, Zhongzhao; Sadat, Umar; Graves, Martin J; Bennett, Martin R; Gillard, Jonathan H

2014-04-11

Compositional and morphological features of carotid atherosclerotic plaques provide complementary information to luminal stenosis in predicting clinical presentations. However, they alone cannot predict cerebrovascular risk. Mechanical stress within the plaque induced by cyclical changes in blood pressure has potential to assess plaque vulnerability. Various modeling strategies have been employed to predict stress, including 2D and 3D structure-only, 3D one-way and fully coupled fluid-structure interaction (FSI) simulations. However, differences in stress predictions using different strategies have not been assessed. Maximum principal stress (Stress-P1) within 8 human carotid atherosclerotic plaques was calculated based on geometry reconstructed from in vivo computerized tomography and high resolution, multi-sequence magnetic resonance images. Stress-P1 within the diseased region predicted by 2D and 3D structure-only, and 3D one-way FSI simulations were compared to 3D fully coupled FSI analysis. Compared to 3D fully coupled FSI, 2D structure-only simulation significantly overestimated stress level (94.1 kPa [65.2, 117.3] vs. 85.5 kPa [64.4, 113.6]; median [inter-quartile range], p=0.0004). However, when slices around the bifurcation region were excluded, stresses predicted by 2D structure-only simulations showed a good correlation (R(2)=0.69) with values obtained from 3D fully coupled FSI analysis. 3D structure-only model produced a small yet statistically significant stress overestimation compared to 3D fully coupled FSI (86.8 kPa [66.3, 115.8] vs. 85.5 kPa [64.4, 113.6]; p<0.0001). In contrast, one-way FSI underestimated stress compared to 3D fully coupled FSI (78.8 kPa [61.1, 100.4] vs. 85.5 kPa [64.4, 113.7]; p<0.0001). A 3D structure-only model seems to be a computationally inexpensive yet reasonably accurate approximation for stress within carotid atherosclerotic plaques with mild to moderate luminal stenosis as compared to fully coupled FSI analysis. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

GPU-Accelerated Forward and Back-Projections with Spatially Varying Kernels for 3D DIRECT TOF PET Reconstruction.

PubMed

Ha, S; Matej, S; Ispiryan, M; Mueller, K

2013-02-01

We describe a GPU-accelerated framework that efficiently models spatially (shift) variant system response kernels and performs forward- and back-projection operations with these kernels for the DIRECT (Direct Image Reconstruction for TOF) iterative reconstruction approach. Inherent challenges arise from the poor memory cache performance at non-axis aligned TOF directions. Focusing on the GPU memory access patterns, we utilize different kinds of GPU memory according to these patterns in order to maximize the memory cache performance. We also exploit the GPU instruction-level parallelism to efficiently hide long latencies from the memory operations. Our experiments indicate that our GPU implementation of the projection operators has slightly faster or approximately comparable time performance than FFT-based approaches using state-of-the-art FFTW routines. However, most importantly, our GPU framework can also efficiently handle any generic system response kernels, such as spatially symmetric and shift-variant as well as spatially asymmetric and shift-variant, both of which an FFT-based approach cannot cope with.

Polydopamine-Coated Magnetic Molecularly Imprinted Polymers with Fragment Template for Identification of Pulsatilla Saponin Metabolites in Rat Feces with UPLC-Q-TOF-MS.

PubMed

Zhang, Yu-Zhen; Zhang, Jia-Wei; Wang, Chong-Zhi; Zhou, Lian-Di; Zhang, Qi-Hui; Yuan, Chun-Su

2018-01-24

In this work, a modified pretreatment method using magnetic molecularly imprinted polymers (MMIPs) was successfully applied to study the metabolites of an important botanical with ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The MMIPs for glucoside-specific adsorption was used to identify metabolites of Pulsatilla chinensis in rat feces. Polymers were prepared by using Fe 3 O 4 nanoparticles as the supporting matrix, d-glucose as fragment template, and dopamine as the functional monomer and cross-linker. Results showed that MMIPs exhibited excellent extraction performance, large adsorption capacity (5.65 mg/g), fast kinetics (60 min), and magnetic separation. Furthermore, the MMIPs coupled with UPLC-Q-TOF-MS were successfully utilized for the identification of 17 compounds including 15 metabolites from the Pulsatilla saponin metabolic pool. This study provides a reliable protocol for the separation and identification of saponin metabolites in a complex biological sample, including those from herbal medicines.

GPU-Accelerated Forward and Back-Projections With Spatially Varying Kernels for 3D DIRECT TOF PET Reconstruction

NASA Astrophysics Data System (ADS)

Ha, S.; Matej, S.; Ispiryan, M.; Mueller, K.

2013-02-01

We describe a GPU-accelerated framework that efficiently models spatially (shift) variant system response kernels and performs forward- and back-projection operations with these kernels for the DIRECT (Direct Image Reconstruction for TOF) iterative reconstruction approach. Inherent challenges arise from the poor memory cache performance at non-axis aligned TOF directions. Focusing on the GPU memory access patterns, we utilize different kinds of GPU memory according to these patterns in order to maximize the memory cache performance. We also exploit the GPU instruction-level parallelism to efficiently hide long latencies from the memory operations. Our experiments indicate that our GPU implementation of the projection operators has slightly faster or approximately comparable time performance than FFT-based approaches using state-of-the-art FFTW routines. However, most importantly, our GPU framework can also efficiently handle any generic system response kernels, such as spatially symmetric and shift-variant as well as spatially asymmetric and shift-variant, both of which an FFT-based approach cannot cope with.

Refractometric detection of liquids using tapered optical fiber and suspended core microstructured fiber: a comparison of methods.

PubMed

Martan, T; Nemecek, T; Komanec, M; Ahmad, R; Zvanovec, S

2017-03-20

Detecting explosive, flammable, or toxic industrial liquids reliably and accurately is a matter of civic responsibility that cannot be treated lightly. Tapered optical fibers (TOFs) and suspended core microstructured optical fibers (SC MOFs) were separately used as sensors of liquids without being compared to each other. We present a highly sensitive time-stable TOF sensor incorporated in the pipeline system for the in-line regime of measurement. This paper is furthermore focused on the comparison of this TOF and SC MOF of similar parameters for the detection of selected liquids. A validated method that incorporates TOF and SC MOF of small core (waist) diameter for refractometric detection is presented. The principle of detection is based on the overlap of an enhanced evanescent wave with a liquid analyte that either fills the cladding holes of the SC MOF or surrounds the waist area of the TOF. Optical power within the evanescent wave for both sensing structures and selected liquid analytes is analyzed. Measurement results concerning TOF and SC MOF are compared. Calculations to ascertain the limit of detection (LOD) for each sensor and the sensitivity (S) to refractive indices of liquid analytes in the range of 1.4269 to 1.4361 were performed at a wavelength of 1550 nm with the lowest refractive index step of 0.0007. Results affirming that S=600.96  dB/RIU and LOD=0.0733  RIU for the SC MOF and S=1143.2  dB/RIU and LOD of 0.0026 RIU for the TOF sensor were achieved, clearly illustrating that TOF-based sensors can reach close to two times greater sensitivity and 30 times higher limit of detection. This paper extends the comparison of the fiber sensors by discussing the potential applications.

Three new isobenzofuranone derivatives from the fruiting bodies of Hericium erinaceus.

PubMed

Wang, Xu-Li; Gao, Jie; Li, Jing; Long, Hong-Ping; Xu, Ping-Sheng; Xu, Kang-Ping; Tan, Gui-Shan

2017-02-01

Three new isobenzofuranone derivatives erinaceolactones D-F (1-3), together with four known ones (4-7), were isolated from the fruiting bodies of Hericium erinaceus. Their structures were determined on the basis of comprehensive spectroscopic analyses including UV, 1D, 2D NMR and HR-TOF-MS. The absolute configuration of erinaceolactone D (1) and erinaceolactone E (2) were assigned by comparing their specific rotation with those of analogs in literatures. The four known compounds were isomers with each other and were isolated simultaneously for the first time.

Unravelling the complex venom landscapes of lethal Australian funnel-web spiders (Hexathelidae: Atracinae) using LC-MALDI-TOF mass spectrometry.

PubMed

Palagi, Alexandre; Koh, Jennifer M S; Leblanc, Mathieu; Wilson, David; Dutertre, Sébastien; King, Glenn F; Nicholson, Graham M; Escoubas, Pierre

2013-03-27

Spider venoms represent vast sources of bioactive molecules whose diversity remains largely unknown. Indeed, only a small subset of species have been studied out of the ~43,000 extant spider species. The present study investigated inter- and intra-species venom complexity in 18 samples collected from a variety of lethal Australian funnel-web spiders (Mygalomorphae: Hexathelidae: Atracinae) using C4 reversed-phase separation coupled to offline MALDI-TOF mass spectrometry (LC-MALDI-TOF MS). An in-depth investigation focusing on four atracine venoms (male Illawarra wisharti, male and female Hadronyche cerberea, and female Hadronyche infensa Toowoomba) revealed, on average, ~800 peptides in female venoms while male venoms contained ~400 peptides, distributed across most HPLC fractions. This is significantly higher than previous estimates of peptide expression in mygalomorph venoms. These venoms also showed distinct intersexual as well as intra- and inter-species variation in peptide masses. Construction of both 3D and 2D contour plots revealed that peptide mass distributions in all 18 venoms were centered around the 3200-5400m/z range and to a lesser extent the 6600-8200m/z range, consistent with previously described hexatoxins. These findings highlight the extensive diversity of peptide toxins in Australian funnel-web spider venoms that that can be exploited as novel therapeutic and biopesticide lead molecules. In the present study we describe the complexity of 18 venoms from lethal Australian funnel-web spiders using LC-MALDI-TOF MS. The study includes an in-depth investigation, focusing on four venoms, that revealed the presence of ~800 peptides in female venoms and ~400 peptides in male venoms. This is significantly higher than previous estimates of peptide expression in spider venoms. By constructing both 3D and 2D contour plots we were also able to reveal the distinct intersexual as well as intra- and inter-species variation in venom peptide masses. We show that peptide mass distributions in all 18 venoms were centered around the 3200-5400 m/z range and to a lesser extent the 6600-8200 m/z range, consistent with the small number of previously described hexatoxins from these spiders. These findings highlight the extensive diversity of peptide toxins in Australian funnel-web spider venoms that that can be exploited as novel therapeutic and biopesticide lead molecules. The present study has greatly expanded our understanding of peptide variety and complexity in these lethal mygalomorph spiders. Specifically it highlights both the utility of LC-MALDI-TOF in spider taxonomy and the massive combinatorial peptide libraries that spider venoms offer the pharmaceutical and agrochemical industry. Copyright © 2013 Elsevier B.V. All rights reserved.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

Quantitative proteomic analysis reveals proteins involved in the neurotoxicity of marine medaka Oryzias melastigma chronically exposed to inorganic mercury.

PubMed

Wang, Yuyu; Wang, Dazhi; Lin, Lin; Wang, Minghua

2015-01-01

Mercury is a ubiquitous environmental contaminant which exerts neurotoxicity upon animals. Nevertheless, the molecular mechanisms involved in inorganic mercury neurotoxicity are unknown. We investigated protein profiles of marine medaka, chronically exposed to mercuric chloride using two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS) analysis. The mercury accumulation and ultrastructure were also examined in the brain. The results showed that mercury was significantly accumulated in the treated brain, and subsequently caused a noticeable damage. The comparison of 2D-DIGE protein profiles between the control and treatment revealed that 16 protein spots were remarkably altered in abundance, which were further submitted for MALDI-TOF-TOF MS analysis. The identified proteins indicated that inorganic mercury may cause neurotoxicity through the induction of oxidative stress, cytoskeletal assembly dysfunction and metabolic disorders. Thus, this study provided a basis for a better understanding of the molecular mechanisms involved in mercury neurotoxicity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simultaneous whole-body time-of-flight 18F-FDG PET/MRI: a pilot study comparing SUVmax with PET/CT and assessment of MR image quality.

PubMed

Iagaru, Andrei; Mittra, Erik; Minamimoto, Ryogo; Jamali, Mehran; Levin, Craig; Quon, Andrew; Gold, Garry; Herfkens, Robert; Vasanawala, Shreyas; Gambhir, Sanjiv Sam; Zaharchuk, Greg

2015-01-01

The recent introduction of hybrid PET/MRI scanners in clinical practice has shown promising initial results for several clinical scenarios. However, the first generation of combined PET/MRI lacks time-of-flight (TOF) technology. Here we report the results of the first patients to be scanned on a completely novel fully integrated PET/MRI scanner with TOF. We analyzed data from patients who underwent a clinically indicated F FDG PET/CT, followed by PET/MRI. Maximum standardized uptake values (SUVmax) were measured from F FDG PET/MRI and F FDG PET/CT for lesions, cerebellum, salivary glands, lungs, aortic arch, liver, spleen, skeletal muscle, and fat. Two experienced radiologists independently reviewed the MR data for image quality. Thirty-six patients (19 men, 17 women, mean [±standard deviation] age of 61 ± 14 years [range: 27-86 years]) with a total of 69 discrete lesions met the inclusion criteria. PET/CT images were acquired at a mean (±standard deviation) of 74 ± 14 minutes (range: 49-100 minutes) after injection of 10 ± 1 mCi (range: 8-12 mCi) of F FDG. PET/MRI scans started at 161 ± 29 minutes (range: 117 - 286 minutes) after the F FDG injection. All lesions identified on PET from PET/CT were also seen on PET from PET/MRI. The mean SUVmax values were higher from PET/MRI than PET/CT for all lesions. No degradation of MR image quality was observed. The data obtained so far using this investigational PET/MR system have shown that the TOF PET system is capable of excellent performance during simultaneous PET/MR with routine pulse sequences. MR imaging was not compromised. Comparison of the PET images from PET/CT and PET/MRI show no loss of image quality for the latter. These results support further investigation of this novel fully integrated TOF PET/MRI instrument.

A highly selective colorimetric and fluorescent chemosensor for Al(III) based-on simple naphthol in aqueous solution

NASA Astrophysics Data System (ADS)

Liu, Zhaodi; Xu, Huajie; Sheng, Liangquan; Chen, Shuisheng; Huang, Deqian; Liu, Jie

2016-03-01

A colorimetric and fluorescent chemosensor (L) for Al(III) was synthesized and fully characterized. L could be both used as a colorimetric and fluorescent chemosensor for the detection of Al3 + ions with low detection limit (8.87 × 10- 7 M) in CH3CN-H2O (1:1, v/v) solution. The binding ratio of L-Al3 + was determined from the Job plot (absorption and fluorescence spectra) and MALDI-TOF MS data to be 1:1. The binding constant (Ka) of Al3 + binding to L was calculated to be 4.8 × 105 M- 1 from a Benesi-Hildebrand plot. Moreover, the binding site of L with Al3 + was determined by 1H NMR titration experiment.

Theory of Synaptic Plasticity in Visual Cortex.

DTIC Science & Technology

1992-12-23

15 Hubel, D. H. and Wiesel, T. N. (1959). Integrative action in the cat’s lateral geniculate body . J. Physiol, 148:574-591. Hubel, D. H. and Wiesel, T...of these afferents derive from the lateral geniculate nucleus (LGN) and from other cortical neurons. We have approached the analysis of this complex...agreement with what is seen experimentally. 3.2 Neurobiological Foundations for the Assumptions of the BCM Theory Recent advances in our understanding of

Effective use of flow-spoiled FBI and time-SLIP methods in the diagnostic study of an aberrant vessel of the head and neck: "left jugular venous steal by the right jugular vein".

PubMed

Kogure, Taroh; Kogure, Kyuya; Iizuka, Mitsumasa; Ino, Azusa; Ishii, Masako

2010-08-01

Three-dimensional (3D) time-of-flight (TOF) is now commonly used in routine magnetic resonance angiography (MRA) studies of the head and neck. However, there are limits to its diagnostic abilities in the clinical field and, in some instances, a more invasive supplementary examination may be required. We incidentally discovered a patient with an aberrant vessel of the head and neck that ran alongside the left carotid artery and contained a constant, slowly pulsating efferent blood flow. 3D-TOF and carotid ultrasonography could not determine the nature and origin of this vessel. Additional studies using flow-spoiled fresh blood imaging (flow-spoiled FBI) and time spatial labeling inversion pulse (time-SLIP) methods were effective in determining that the vessel was the left jugular vein, and that the continuous venous reflux was a result of a venous steal by the right jugular vein. We show that by combining different MRA techniques we can effectively achieve diagnosis without resorting to more invasive examinations. 2010 Wiley-Liss, Inc.

PMT-scintillator system set up for D-D neutron TOF measurements in INTI plasma focus device

NASA Astrophysics Data System (ADS)

Damideh, V.; Saw, S. H.; Sadighzadeh, A.; Ali, J.; Rawat, R. S.; Lee, P.; Lee, S.

2017-03-01

This paper summarizes a Photomultiplier-Scintillator diagnostic system for use in our plasma focus experiments at the Center for Plasma Research INTI IU. The system features an anode-grounded high pulse linearity voltage divider and uses NE102A plastic scintillators. It has detected D-D neutrons in INTI plasma focus device with clear and high signal to noise ratio. Neutron TOF of 120 ns has been measured from the time difference between hard x-ray pulse peak and neutron peak time over a flight path of 2.6±0.01 m; giving energy of 2.5±0.1 MeV for these side-on neutrons.

Deuterated-xylene (xylene-d10; EJ301D): A new, improved deuterated liquid scintillator for neutron energy measurements without time-of-flight

NASA Astrophysics Data System (ADS)

Becchetti, F. D.; Raymond, R. S.; Torres-Isea, R. O.; Di Fulvio, A.; Clarke, S. D.; Pozzi, S. A.; Febbraro, M.

2016-06-01

In conjunction with Eljen Technology, Inc. (Sweetwater,TX) we have designed, constructed, and evaluated a 3 in. ×3 in. deuterated-xylene organic liquid scintillator (C8D10; EJ301D) as a fast neutron detector. Similar to deuterated benzene (C6D6; NE230, BC537, and EJ315) this scintillator can provide good pulse-shape discrimination between neutrons and gamma rays, has good timing characteristics, and can provide a light spectrum with peaks corresponding to discrete neutron energy groups up to ca. 20 MeV. Unlike benzene-based detectors, deuterated xylene is less volatile, less toxic, is not known to be carcinogenic, has a higher flashpoint, and hence is much safer for many applications. In addition EJ301D can provide slightly more light output and better PSD than deuterated-benzene scintillators. We show that, as with deuterated-benzene scintillators, the light-response spectra can be unfolded to provide useable neutron energy spectra without need for time-of-flight (ToF). An array of these detectors arranged at many angles close to a reaction target can be much more effective (×10 to ×100 or more) than an array of long-path ToF detectors which must utilize a narrowly-bunched and pulse-selected beam. As we demonstrate using a small Van de Graaff accelerator, measurements can thus be performed when a bunched and pulse-selected beam (as needed for time-of-flight) is not available.

Remarkable NO oxidation on single supported platinum atoms

DOE PAGES

Narula, Chaitanya K.; Allard, Lawrence F.; Stocks, G. M.; ...

2014-11-28

Our first-principles density functional theoretical modeling suggests that NO oxidation is feasible on fully oxidized single θ-alumina-supported platinum atoms via a modified Langmuir-Hinshelwood pathway. This is in contrast to the known decrease in NO oxidation activity of supported platinum with decreasing Pt particle size believed to be due to increased platinum oxidation. In order to validate our theoretical study, we evaluated single θ-Al 2O 3-supported platinum atoms and found them to exhibit remarkable NO oxidation activity. A comparison of turnover frequencies (TOF) of single supported Pt atoms with those of platinum particles for NO oxidation shows that single supported Ptmore » atoms are as active as fully formed platinum particles. The overall picture of NO oxidation on supported Pt is that NO oxidation activity decreases with decreasing Pt particle size but accelerates when Pt is present only as single atoms.« less

Identification of rutin deglycosylated metabolites produced by human intestinal bacteria using UPLC-Q-TOF/MS.

PubMed

Yang, Jing; Qian, Dawei; Jiang, Shu; Shang, Er-xin; Guo, Jianming; Duan, Jin-ao

2012-06-01

In this paper, rutin was metabolized by human intestinal bacteria and five isolated strains including Bacillus sp. 52, Bacteroides sp. 45, 42, 22 and Veillonella sp. 32, the metabolites were identified using ultra performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS). As a result, Bacillus sp. 52 and Bacteroides sp. 45 could metabolize rutin to quercetin 3-O-glucoside and leucocyanidin. Bacteroides sp. 42 and Veillonella sp. 32 could convert rutin to leucocyanidin. Bacteroides sp. 22 could hydrolyze rutin to quercetin-3-O-glucoside. In order to further explain the metabolism pathway of rutin, the β-D-glucosidase and α-L-rhamnosidase activities of five strains were determined. Bacteroides sp. 22 could produce α-L-rhamnosidase but did not produce β-D-glucosidase or β-D-glucosidase activity was too low to be detected. The other four strains all demonstrated α-L-rhamnosidase and β-D-glucosidase activities. Furthermore, α-L-rhamnosidase and β-D-glucosidase activities of Veillonella sp. 32 and Bacteroides sp. 42 were higher than those of Bacteroides sp. 45 and Bacillus sp. 52. Based on these results, we can propose the deglycosylated rout of rutin: rutin was metabolized to be quercetin-3-O-glucoside by α-L-rhamnosidase produced from these bacteria, thereafter, quercetin-3-O-glucoside was further metabolized by β-D-glucosidase to form leucocyanidin. Because of the higher enzyme activity in Veillonella sp. 32 and Bacteroides sp. 42, quercetin-3-O-glucoside was completely metabolized to leucocyanidin by these two bacteria. Due to the lack of β-D-glucosidase activity, Bacteroides sp. 22 could not further metabolize quercetin-3-O-glucoside to leucocyanidin. This study will be helpful for understanding the deglycosylated rout of rutin and the role of different intestinal bacteria on the metabolism of natural compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis and Spectroscopic Evaluation of Two Novel Glycosylated Zinc(II)-Phthalocyanines.

PubMed

Bächle, Felix; Hanack, Michael; Ziegler, Thomas

2015-10-09

In continuation of our work on glycoconjugated phthalocyanines, two new water soluble, non-ionic zinc(II) phthalocyanines have been prepared and fully characterized by means of ¹H-NMR, 13C-NMR, MALDI-TOF, ESI-TOF, UV-Vis spectroscopy, emission spectroscopy and fluorescence lifetime measurements. The carbohydrate-containing phthalonitrile precursors were synthesized through a copper-catalyzed azide-alkyne cycloaddition (CuAAC). The 2-methoxyethoxymethyl protecting group (MEM) was used to protect the carbohydrate moieties. It resisted the harsh basic cyclotetramerization conditions and could be easily cleaved under mild acidic conditions. The glycoconjugated zinc(II) phthalocyanines described here have molar extinction coefficents εmax>10⁵ m(-1) cm(-1) and absorption maxima λ>680 nm, which make them attractive photosensitizers for photo-dynamic therapy.

Testing a new NIF neutron time-of-flight detector with a bibenzyl scintillator on OMEGA.

PubMed

Glebov, V Yu; Forrest, C; Knauer, J P; Pruyne, A; Romanofsky, M; Sangster, T C; Shoup, M J; Stoeckl, C; Caggiano, J A; Carman, M L; Clancy, T J; Hatarik, R; McNaney, J; Zaitseva, N P

2012-10-01

A new neutron time-of-flight (nTOF) detector with a bibenzyl crystal as a scintillator has been designed and manufactured for the National Ignition Facility (NIF). This detector will replace a nTOF20-Spec detector with an oxygenated xylene scintillator currently operational on the NIF to improve the areal-density measurements. In addition to areal density, the bibenzyl detector will measure the D-D and D-T neutron yield and the ion temperature of indirect- and direct-drive-implosion experiments. The design of the bibenzyl detector and results of tests on the OMEGA Laser System are presented.

Evaluating The Relation of Trace Fracture Inclination and Sound Pressure Level and Time-of-flight QUS Parameters Using Computational Simulation

NASA Astrophysics Data System (ADS)

Rosa, P. T.; Fontes-Pereira, A. J.; Matusin, D. P.; von Krüger, M. A.; Pereira, W. C. A.

Bone healing is a complex process that stars after the occurrence of a fracture to restore bone optimal conditions. The gold standards for bone status evaluation are the dual energy X-ray absorptiometry and the computerized tomography. Ultrasound-based technologies have some advantages as compared to X-ray technologies: nonionizing radiation, portability and lower cost among others. Quantitative ultrasound (QUS) has been proposed in literature as a new tool to follow up the fracture healing process. QUS relates the ultrasound propagation with the bone tissue condition (normal or pathological), so, a change in wave propagation may indicate a variation in tissue properties. The most used QUS parameters are time-of-flight (TOF) and sound pressure level (SPL) of the first arriving signal (FAS). In this work, the FAS is the well known lateral wave. The aim of this work is to evaluate the relation of the TOF and SPL of the FAS and fracture inclination trace in two stages of bone healing using computational simulations. Four fracture geometries were used: normal and oblique with 30, 45 and 60 degrees. The TOF average values were 63.23 μs, 63.14 μs, 63.03 μs 62.94 μs for normal, 30, 45 and 60 degrees respectively and average SPL values were -3.83 dB -4.32 dB, -4.78 dB, -6.19 dB for normal, 30, 45 and 60 degrees respectively. The results show an inverse pattern between the amplitude and time-of-flight. These values seem to be sensible to fracture inclination trace, and in future, can be used to characterize it.

Quantitative and Qualitative Assessment of Yttrium-90 PET/CT Imaging

PubMed Central

Büsing, Karen-Anett; Schönberg, Stefan O.; Bailey, Dale L.; Willowson, Kathy; Glatting, Gerhard

2014-01-01

Yttrium-90 is known to have a low positron emission decay of 32 ppm that may allow for personalized dosimetry of liver cancer therapy with 90Y labeled microspheres. The aim of this work was to image and quantify 90Y so that accurate predictions of the absorbed dose can be made. The measurements were performed within the QUEST study (University of Sydney, and Sirtex Medical, Australia). A NEMA IEC body phantom containing 6 fillable spheres (10–37 mm ∅) was used to measure the 90Y distribution with a Biograph mCT PET/CT (Siemens, Erlangen, Germany) with time-of-flight (TOF) acquisition. A sphere to background ratio of 8∶1, with a total 90Y activity of 3 GBq was used. Measurements were performed for one week (0, 3, 5 and 7 d). he acquisition protocol consisted of 30 min-2 bed positions and 120 min-single bed position. mages were reconstructed with 3D ordered subset expectation maximization (OSEM) and point spread function (PSF) for iteration numbers of 1–12 with 21 (TOF) and 24 (non-TOF) subsets and CT based attenuation and scatter correction. Convergence of algorithms and activity recovery was assessed based on regions-of-interest (ROI) analysis of the background (100 voxels), spheres (4 voxels) and the central low density insert (25 voxels). For the largest sphere, the recovery coefficient (RC) values for the 30 min –2-bed position, 30 min-single bed and 120 min-single bed were 1.12±0.20, 1.14±0.13, 0.97±0.07 respectively. For the smaller diameter spheres, the PSF algorithm with TOF and single bed acquisition provided a comparatively better activity recovery. Quantification of Y-90 using Biograph mCT PET/CT is possible with a reasonable accuracy, the limitations being the size of the lesion and the activity concentration present. At this stage, based on our study, it seems advantageous to use different protocols depending on the size of the lesion. PMID:25369020

Identified hadron spectra from PHOBOS

NASA Astrophysics Data System (ADS)

Veres, Gábor I.; the PHOBOS Collaboration; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Becker, B.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Harrington, A. S.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lee, J. W.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Sarin, P.; Sedykh, I.; Skulski, W.; Smith, C. E.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wolfs, F. L. H.; Wosiek, B.; Wozniak, K.; Wysłouch, B.; Zhang, J.

2004-08-01

Transverse momentum spectra of pions, kaons and protons, as well as antiparticle to particle ratios near mid-rapidity from d+Au collisions at \\sqrt{sNN} = 200 GeV have been measured by the PHOBOS experiment at RHIC. The transverse momentum range of particle identification was extended to beyond 3 GeV/c using the TOF detector and a new trigger system. The pseudorapidity dependence of the nuclear modification factor for charged hadrons in d+Au collisions is presented.

Identified hadron spectra from PHOBOS

NASA Astrophysics Data System (ADS)

Veres, Gábor I.; PHOBOS Collaboration; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Becker, B.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Harrington, A. S.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Holynski, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lee, J. W.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Sarin, P.; Sedykh, I.; Skulski, W.; Smith, C. E.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wolfs, F. L. H.; Wosiek, B.; Wozniak, K.; Wyslouch, B.; Zhang, J.

2004-08-01

Transverse momentum spectra of pions, kaons and protons, as well as antiparticle to particle ratios near mid-rapidity from d+Au collisions at \\sqrt{s_{{\\rm NN}}} = 200\\,{\\rm GeV} have been measured by the PHOBOS experiment at RHIC. The transverse momentum range of particle identification was extended to beyond 3 GeV/c using the TOF detector and a new trigger system. The pseudorapidity dependence of the nuclear modification factor for charged hadrons in d+Au collisions is presented.

P185-M Protein Identification and Validation of Results in Workflows that Integrate over Various Instruments, Datasets, Search Engines

PubMed Central

Hufnagel, P.; Glandorf, J.; Körting, G.; Jabs, W.; Schweiger-Hufnagel, U.; Hahner, S.; Lubeck, M.; Suckau, D.

2007-01-01

Analysis of complex proteomes often results in long protein lists, but falls short in measuring the validity of identification and quantification results on a greater number of proteins. Biological and technical replicates are mandatory, as is the combination of the MS data from various workflows (gels, 1D-LC, 2D-LC), instruments (TOF/TOF, trap, qTOF or FTMS), and search engines. We describe a database-driven study that combines two workflows, two mass spectrometers, and four search engines with protein identification following a decoy database strategy. The sample was a tryptically digested lysate (10,000 cells) of a human colorectal cancer cell line. Data from two LC-MALDI-TOF/TOF runs and a 2D-LC-ESI-trap run using capillary and nano-LC columns were submitted to the proteomics software platform ProteinScape. The combined MALDI data and the ESI data were searched using Mascot (Matrix Science), Phenyx (GeneBio), ProteinSolver (Bruker and Protagen), and Sequest (Thermo) against a decoy database generated from IPI-human in order to obtain one protein list across all workflows and search engines at a defined maximum false-positive rate of 5%. ProteinScape combined the data to one LC-MALDI and one LC-ESI dataset. The initial separate searches from the two combined datasets generated eight independent peptide lists. These were compiled into an integrated protein list using the ProteinExtractor algorithm. An initial evaluation of the generated data led to the identification of approximately 1200 proteins. Result integration on a peptide level allowed discrimination of protein isoforms that would not have been possible with a mere combination of protein lists.

Dehydrogenation and dehalogenation of amines in MALDI-TOF MS investigated by isotopic labeling.

PubMed

Kang, Chuanqing; Zhou, Yihan; Du, Zhijun; Bian, Zheng; Wang, Jianwei; Qiu, Xuepeng; Gao, Lianxun; Sun, Yuequan

2013-12-01

Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules. Copyright © 2013 John Wiley & Sons, Ltd.

Implant-specific follow-up imaging of treated intracranial aneurysms: TOF-MRA vs. metal artifact reduced intravenous flat panel computed tomography angiography (FPCTA).

PubMed

Hänsel, N H; Schubert, G A; Scholz, B; Nikoubashman, O; Othman, A E; Wiesmann, M; Pjontek, R; Brockmann, M A

2018-02-01

To compare the diagnostic quality of time-of-flight magnetic resonance angiography (TOF-MRA) and metal-artefact-reduction (MAR) flat-panel-detector computed tomography angiography (FPCTA) and to determine the imaging technique best suited for evaluation endovascular and surgically treated aneurysms. The image quality of TOF-MRA and MAR-FPCTA of 44 intracranial implants (coiling: n=20; clipping: n=15; coiling + stenting: n=9) in a patient cohort of 25 was evaluated by two independent readers. Images obtained using MAR-FPCTA (20 second scan time, 496 projections, intravenous contrast medium administration; Artis Zee, Siemens Healthcare, Forchheim) were compared with TOF-MRA-images (1.5 or 3 T). Nominal data were analysed using McNemar's chi-square test and ordinal variables using the Wilcoxon rank test. Compared to TOF-MRA, MAR-FPCTA was significantly better suited to detect aneurysm remnants and to evaluate parent vessels after clipping (p<0.01). For coil packages >160 mm 3 , TOF-MRA provided significantly better assessment than MAR-FPCTA (p<0.01). For small coil packages (<160 mm 3 ), no significant difference between TOF-MRA and MAR-FPCTA (p=0.232) was observed. For different clip sizes (cut-off 492 mm 3 ) likewise no significant differences were found. The interobserver comparison showed high interrater agreement. MAR-FPCTA is significantly better suited for follow-up examinations of clipped aneurysms, whereas for larger coil packages TOF-MRA is preferable. Smaller coil packages can be analysed using MAR-FPCTA or TOF-MRA. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species

PubMed Central

Suttisunhakul, Vichaya; Pumpuang, Apinya; Ekchariyawat, Peeraya; Wuthiekanun, Vanaporn; Elrod, Mindy G.; Turner, Paul; Currie, Bart J.; Phetsouvanh, Rattanaphone; Dance, David A. B.; Limmathurotsakul, Direk; Peacock, Sharon J.

2017-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species. PMID:28384252

Castings, Steel, Homogenization of Steel Castings

DTIC Science & Technology

1942-12-05

concerninr.. the ef- fe~ct of homogenizing herat-- treAment u-non the ballistic prop- erties -%f cLast steel armo--iercinr nrro jectilt:s. .arden.YD- 1 t...of hLmogenizing- treAments upon the3 corrosi;.A -.f quenched- Lr(- t c,-.rnered. c-.st steel. Harich, Riffin, -ri Bolotsk-2 .. ade two-bec-d weldahtil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuermann, Karl; Vorwerk, Dierk; Buecker, Arno

Purpose: To compare nonferromagnetic iliac artery prostheses in their suitability for patency monitoring with magnetic resonance angiography (MRA) using conventional angiography as a reference. Methods: In experiment 1, three Memotherm stents were inserted into the iliac arteries of each of six sheep: two 'tandem' stents on one side and a single stent on the other side. In experiment 2, four prostheses (normal and low-porosity Corvita stent-grafts, Memotherm, ZA-stent) were inserted in each of 11 sheep. Patency was monitored before and 1, 3, and 6 months after insertion with 3D phase-contrast and two 2D time-of-flight sequences (TOF-1: TR/TE = 18/6.9, TOF-2:more » 13/2.5) with and without contrast at 1.5 T. On 206 coronal MIP images (72 pre-, 134 post-stenting), three readers analyzed 824 iliac segments (206 x 4) for patency and artifacts. Results: There was no difference in the number of artifacts between tandem and single iliac Memotherm stents. The ZA-stent induced significantly fewer artifacts than the other prostheses (p < 0.00001). With MRA, patency of the ZA-stent was correctly diagnosed in 88% of cases, which was almost comparable to nonstented iliac segments (95%), patency of the Memotherm stent in 59%, and of the Corvita stent-grafts in 57% and 55%. The TOF-2 sequence with contrast yielded the best images. Conclusion: MRA compatibility of nonferromagnetic prostheses depends strongly on the design of the device. MRA may be used to monitor the patency of iliac ZA-stents, whereas iliac Memotherm stents and Corvita stent-grafts appear to be less suited for follow-up with MRA.« less

Real-time image processing of TOF range images using a reconfigurable processor system

NASA Astrophysics Data System (ADS)

Hussmann, S.; Knoll, F.; Edeler, T.

2011-07-01

During the last years, Time-of-Flight sensors achieved a significant impact onto research fields in machine vision. In comparison to stereo vision system and laser range scanners they combine the advantages of active sensors providing accurate distance measurements and camera-based systems recording a 2D matrix at a high frame rate. Moreover low cost 3D imaging has the potential to open a wide field of additional applications and solutions in markets like consumer electronics, multimedia, digital photography, robotics and medical technologies. This paper focuses on the currently implemented 4-phase-shift algorithm in this type of sensors. The most time critical operation of the phase-shift algorithm is the arctangent function. In this paper a novel hardware implementation of the arctangent function using a reconfigurable processor system is presented and benchmarked against the state-of-the-art CORDIC arctangent algorithm. Experimental results show that the proposed algorithm is well suited for real-time processing of the range images of TOF cameras.

Time-of-flight scattering and recoiling spectrometer (TOF-SARS) for surface analysis

NASA Astrophysics Data System (ADS)

Grizzi, O.; Shi, M.; Bu, H.; Rabalais, J. W.

1990-02-01

A UHV spectrometer system has been designed and constructed for time-of-flight scattering and recoiling spectrometry (TOF-SARS). The technique uses a pulsed primary ion beam and TOF methods for analysis of both scattered and recoiled neutrals (N) and ions (I) simultaneously with continuous scattering angle variation over a flight path of ≊1 m. The pulsed ion beam line uses an electron impact ionization source with acceleration up to 5 keV; pulse widths down to 20 ns with average current densities of 0.05-5.0 nA/mm2 have been obtained. Typical current densities used herein are ≊0.1 nA/mm2 and TOF spectra can be collected with a total ion dose of <10-3 ions/surface atom. A channel electron multiplier detector, which is sensitive to both ions and fast neutrals, is mounted on a long tube connected to a precision rotary motion feedthru, allowing continuous rotation over a scattering angular range 0°<θ<165°. The sample is mounted on a precision manipulator, allowing azimuthal δ and incident α angle rotation, as well as translation along three orthogonal axes. The system also accommodates standard surface analysis instrumentation for LEED, AES, XPS, and UPS. The capabilities of the system are demonstrated by the following examples: (A) TOF spectra versus scattering angle θ; (B) comparison to LEED and AES; (C) surface and adsorbate structure determinations; (D) monitoring surface roughness; (E) surface semichanneling measurements; (F) measurements of scattered ion fractions; and (G) ion induced Auger electron emission.

Ultrasound indoor positioning system based on a low-power wireless sensor network providing sub-centimeter accuracy.

PubMed

Medina, Carlos; Segura, José Carlos; De la Torre, Ángel

2013-03-13

This paper describes the TELIAMADE system, a new indoor positioning system based on time-of-flight (TOF) of ultrasonic signal to estimate the distance between a receiver node and a transmitter node. TELIAMADE system consists of a set of wireless nodes equipped with a radio module for communication and a module for the transmission and reception of ultrasound. The access to the ultrasonic channel is managed by applying a synchronization algorithm based on a time-division multiplexing (TDMA) scheme. The ultrasonic signal is transmitted using a carrier frequency of 40 kHz and the TOF measurement is estimated by applying a quadrature detector to the signal obtained at the A/D converter output. Low sampling frequencies of 17.78 kHz or even 12.31 kHz are possible using quadrature sampling in order to optimize memory requirements and to reduce the computational cost in signal processing. The distance is calculated from the TOF taking into account the speed of sound. An excellent accuracy in the estimation of the TOF is achieved using parabolic interpolation to detect of maximum of the signal envelope at the matched filter output. The signal phase information is also used for enhancing the TOF measurement accuracy. Experimental results show a root mean square error (rmse) less than 2 mm and a standard deviation less than 0.3 mm for pseudorange measurements in the range of distances between 2 and 6 m. The system location accuracy is also evaluated by applying multilateration. A sub-centimeter location accuracy is achieved with an average rmse of 9.6 mm.

Purification, characterization, and substrate specificity of a glucoamylase with steroidal saponin-rhamnosidase activity from Curvularia lunata.

PubMed

Feng, Bing; Hu, Wei; Ma, Bai-ping; Wang, Yong-ze; Huang, Hong-ze; Wang, Sheng-qi; Qian, Xiao-hong

2007-10-01

It has been previously reported that a glucoamylase from Curvularia lunata is able to hydrolyze the terminal 1,2-linked rhamnosyl residues of sugar chains at C-3 position of steroidal saponins. In this work, the enzyme was isolated and identified after isolation and purification by column chromatography including gel filtration and ion-exchange chromatography. Analysis of protein fragments by MALDI-TOF/TOF proteomics Analyzer indicated the enzyme to be 1,4-alpha-D-glucan glucohydrolase EC 3.2.1.3, GA and had considerable homology with the glucoamylase from Aspergillus oryzae. We first found that the glucoamylase was produced from C. lunata and was able to hydrolyze the terminal rhamnosyl of steroidal saponins. The enzyme had the general character of glucoamylase, which hydrolyze starch. It had a molecular mass of 66 kDa and was optimally active at 50 degrees C, pH 4, and specific activity of 12.34 U mg of total protein(-1) under the conditions, using diosgenin-3-O-alpha-L-rhamnopyranosyl(1-->4)-[alpha-L-rhamnopyranosyl (1-->2)]-beta-D-glucopyranoside (compound II) as the substrate. Furthermore, four kinds of commercial glucoamylases from Aspergillus niger were investigated in this work, and they had the similar activity in hydrolyzing terminal rhamnosyl residues of steroidal saponin.

[EXPRESS IDENTIFICATION OF POSITIVE BLOOD CULTURES USING DIRECT MALDI-TOF MASS SPECTROMETRY].

PubMed

Popov, D A; Ovseenko, S T; Vostrikova, T Yu

2015-01-01

To evaluate the effectiveness of direct identification of pathogens of bacteremia by direct matrix assisted laser desorption ionization time-flight mass spectrometry (mALDI-TOF) compared to routine method. A prospective study included 211 positive blood cultures obtained from 116 patients (106 adults and 10 children, aged from 2 weeks to 77 years old in the ICU after open heart surgery. Incubation was carried out under aerobic vials with a sorbent for antibiotics Analyzer BacT/ALERT 3D 120 (bioMerieux, France) in parallel with the primary sieving blood cultures on solid nutrient media with subsequent identification of pure cultures using MALDI-TOF mass spectrometry analyzer Vitek MS, bioMerieux, France routine method), after appropriate sample preparation we carried out a direct (without screening) MALDI-TOF mass spectrometric study of monocomponental blood cultures (n = 201). using a routine method in 211 positive blood cultures we identified 23 types of microorganisms (Staphylococcus (n = 87), Enterobacteria- ceae (n = 71), Enterococci (n = 20), non-fermentative Gram-negative bacteria (n = 18), others (n = 5). The average time of incubation of samples to obtain a signal of a blood culture growth was 16.2 ± 7.4 h (from 3.75 to 51 hours.) During the first 12 hours of incubation, growth was obtained in 32.4% of the samples, and on the first day in 92.2%. In the direct mass spectrometric analysis mnonocomponental blood cultures (n = 201) is well defined up to 153 species of the sample (76.1%), while the share of successful identification of Gram-negative bacteria was higher than that of Gram-positive (85.4 and 69, 1%, respectively p = 0.01). The high degree of consistency in the results of standard and direct method of identifying blood cultures using MALDI-TOF mass spectrometry (κ = 0.96, p < 0.001; the samples included in the calculation for which both option given result). Duration of the direct mass spectrometric analysis, including sample preparation, was no longer than 1 hour: The method of direct MALDI-TOF mass spectrometry allows to significantly speed up the identification of blood cultures that may contribute as much as possible early appointment effective regimes of starting antibiotic therapy.

The measurement programme at the neutron time-of-flight facility n_TOF at CERN

NASA Astrophysics Data System (ADS)

Gunsing, F.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Bacak, M.; Balibrea-Correa, J.; Barbagallo, M.; Barros, S.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brown, A.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Colonna, N.; Cortés-Giraldo, M. A.; Cortés, G.; Cosentino, L.; Damone, L. A.; Deo, K.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Frost, R. J. W.; Furman, V.; Ganesan, S.; García, A. R.; Gawlik, A.; Gheorghe, I.; Gilardoni, S.; Glodariu, T.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Griesmayer, E.; Guerrero, C.; Göbel, K.; Harada, H.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Kalamara, A.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Kurtulgil, D.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lerendegui, J.; Licata, M.; Meo, S. Lo; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Musumarra, A.; Nolte, R.; Negret, A.; Oprea, A.; Palomo-Pinto, F. R.; Paradela, C.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Quesada, J. M.; Radeck, D.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Rout, P.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Sosnin, N. V.; Stamatopoulos, A.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Weiss, C.; Wolf, C.; Woods, P. J.; Wright, T.; Žugec, P.

2017-09-01

Neutron-induced reaction cross sections are important for a wide variety of research fields ranging from the study of nuclear level densities, nucleosynthesis to applications of nuclear technology like design, and criticality and safety assessment of existing and future nuclear reactors, radiation dosimetry, medical applications, nuclear waste transmutation, accelerator-driven systems and fuel cycle investigations. Simulations and calculations of nuclear technology applications largely rely on evaluated nuclear data libraries. The evaluations in these libraries are based both on experimental data and theoretical models. CERN's neutron time-of-flight facility n_TOF has produced a considerable amount of experimental data since it has become fully operational with the start of its scientific measurement programme in 2001. While for a long period a single measurement station (EAR1) located at 185 m from the neutron production target was available, the construction of a second beam line at 20 m (EAR2) in 2014 has substantially increased the measurement capabilities of the facility. An outline of the experimental nuclear data activities at n_TOF will be presented.

Comprehensive Optimization of LC-MS Metabolomics Methods Using Design of Experiments (COLMeD).

PubMed

Rhoades, Seth D; Weljie, Aalim M

2016-12-01

Both reverse-phase and HILIC chemistries are deployed for liquid-chromatography mass spectrometry (LC-MS) metabolomics analyses, however HILIC methods lag behind reverse-phase methods in reproducibility and versatility. Comprehensive metabolomics analysis is additionally complicated by the physiochemical diversity of metabolites and array of tunable analytical parameters. Our aim was to rationally and efficiently design complementary HILIC-based polar metabolomics methods on multiple instruments using Design of Experiments (DoE). We iteratively tuned LC and MS conditions on ion-switching triple quadrupole (QqQ) and quadrupole-time-of-flight (qTOF) mass spectrometers through multiple rounds of a workflow we term COLMeD (Comprehensive optimization of LC-MS metabolomics methods using design of experiments). Multivariate statistical analysis guided our decision process in the method optimizations. LC-MS/MS tuning for the QqQ method on serum metabolites yielded a median response increase of 161.5% (p<0.0001) over initial conditions with a 13.3% increase in metabolite coverage. The COLMeD output was benchmarked against two widely used polar metabolomics methods, demonstrating total ion current increases of 105.8% and 57.3%, with median metabolite response increases of 106.1% and 10.3% (p<0.0001 and p<0.05 respectively). For our optimized qTOF method, 22 solvent systems were compared on a standard mix of physiochemically diverse metabolites, followed by COLMeD optimization, yielding a median 29.8% response increase (p<0.0001) over initial conditions. The COLMeD process elucidated response tradeoffs, facilitating improved chromatography and MS response without compromising separation of isobars. COLMeD is efficient, requiring no more than 20 injections in a given DoE round, and flexible, capable of class-specific optimization as demonstrated through acylcarnitine optimization within the QqQ method.

Comprehensive Optimization of LC-MS Metabolomics Methods Using Design of Experiments (COLMeD)

PubMed Central

Rhoades, Seth D.

2017-01-01

Introduction Both reverse-phase and HILIC chemistries are deployed for liquid-chromatography mass spectrometry (LC-MS) metabolomics analyses, however HILIC methods lag behind reverse-phase methods in reproducibility and versatility. Comprehensive metabolomics analysis is additionally complicated by the physiochemical diversity of metabolites and array of tunable analytical parameters. Objective Our aim was to rationally and efficiently design complementary HILIC-based polar metabolomics methods on multiple instruments using Design of Experiments (DoE). Methods We iteratively tuned LC and MS conditions on ion-switching triple quadrupole (QqQ) and quadrupole-time-of-flight (qTOF) mass spectrometers through multiple rounds of a workflow we term COLMeD (Comprehensive optimization of LC-MS metabolomics methods using design of experiments). Multivariate statistical analysis guided our decision process in the method optimizations. Results LC-MS/MS tuning for the QqQ method on serum metabolites yielded a median response increase of 161.5% (p<0.0001) over initial conditions with a 13.3% increase in metabolite coverage. The COLMeD output was benchmarked against two widely used polar metabolomics methods, demonstrating total ion current increases of 105.8% and 57.3%, with median metabolite response increases of 106.1% and 10.3% (p<0.0001 and p<0.05 respectively). For our optimized qTOF method, 22 solvent systems were compared on a standard mix of physiochemically diverse metabolites, followed by COLMeD optimization, yielding a median 29.8% response increase (p<0.0001) over initial conditions. Conclusions The COLMeD process elucidated response tradeoffs, facilitating improved chromatography and MS response without compromising separation of isobars. COLMeD is efficient, requiring no more than 20 injections in a given DoE round, and flexible, capable of class-specific optimization as demonstrated through acylcarnitine optimization within the QqQ method. PMID:28348510

Efficient identification of Malassezia yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

PubMed

Kolecka, A; Khayhan, K; Arabatzis, M; Velegraki, A; Kostrzewa, M; Andersson, A; Scheynius, A; Cafarchia, C; Iatta, R; Montagna, M T; Youngchim, S; Cabañes, F J; Hoopman, P; Kraak, B; Groenewald, M; Boekhout, T

2014-02-01

Infections caused by Malassezia yeasts are most likely underdiagnosed, because fatty acid supplementation is needed for growth. Rapid identification of Malassezia species is essential for appropriate treatment of Malassezia-related skin infections, fungaemia and nosocomial outbreaks in neonates, children and adults and can be life-saving for those patients. Ma-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a rapid and reliable diagnostic tool to identify clinically important yeasts, but so far no data have been reported on identification of Malassezia isolates with this technique. To create an extensive database of main mass spectra (MSPs) that will allow quick identification of Malassezia species by MALDI-TOF MS. An in-house library of 113 MSPs was created from 48 reference strains from the CBS-KNAW yeast collection. The in-house library was challenged with two test sets of Malassezia strains, namely 165 reference strains from the CBS collection and 338 isolates collected in Greece, Italy, Sweden and Thailand. MALDI-TOF MS allowed correct identification of all 14 Malassezia spp. MALDI-TOF MS results were concordant with those of sequence analyses of the internal transcribed spacers (ITS1/ITS2) and the D1/D2 domains of the large subunit of the ribosomal DNA. Implementation of the MALDI-TOF MS system as a routine identification tool will contribute to correct identification of Malassezia yeasts with minimal effort and in a short turnaround time, which is especially important for the rapid identification of Malassezia in skin diseases and nosocomial outbreaks. © 2013 British Association of Dermatologists.

Application of 2-dimensional difference gel electrophoresis (2D-DIGE) to the study of thrombin-activated human platelet secretome.

PubMed

Della Corte, Anna; Maugeri, Norma; Pampuch, Agnieszka; Cerletti, Chiara; de Gaetano, Giovanni; Rotilio, Domenico

2008-02-01

Thrombin is an agonist inducing platelet activation. We combined two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry (MALDI-TOF MS) to analyse differentially expressed proteins secreted from thrombin-stimulated platelets. Human washed platelets, from healthy volunteers, were stimulated with thrombin 0.5 U/ml at 37 degrees C without stirring and the secreted proteins were resolved by 2D-DIGE. By image analysis, 1094 spots were detected in the 2D gel. The spots whose mean intensity showed at least a five-fold change intensity increase or decrease in the thrombin-activated platelet gel in comparison with unstimulated control were digested by trypsin and subjected to MALDI-TOF MS analysis. Peptides from mass spectra of in-gel digest samples were matched against available databases, using the Mascot search engine (Matrix Science) for peptide mass fingerprint. In the activated platelet secretome, transferrin, glutathione-transferase, WD repeat protein, ER-60, thrombospondin-1 precursor and thrombospondin were the most abundant. Also lamin A, a nuclear protein, not previously identified in platelets, appeared to be released. The novel strategy to combine 2D-DIGE with MALDI-TOF MS is a useful approach for a quantitative analysis of the effect of thrombin on the secretome profile of human platelets.

Prospective PET image quality gain calculation method by optimizing detector parameters.

PubMed

Theodorakis, Lampros; Loudos, George; Prassopoulos, Vasilios; Kappas, Constantine; Tsougos, Ioannis; Georgoulias, Panagiotis

2015-12-01

Lutetium-based scintillators with high-performance electronics introduced time-of-flight (TOF) reconstruction in the clinical setting. Let G' be the total signal to noise ratio gain in a reconstructed image using the TOF kernel compared with conventional reconstruction modes. G' is then the product of G1 gain arising from the reconstruction process itself and (n-1) other gain factors (G2, G3, … Gn) arising from the inherent properties of the detector. We calculated G2 and G3 gains resulting from the optimization of the coincidence and energy window width for prompts and singles, respectively. Both quantitative and image-based validated Monte Carlo models of Lu2SiO5 (LSO) TOF-permitting and Bi4Ge3O12 (BGO) TOF-nonpermitting detectors were used for the calculations. G2 and G3 values were 1.05 and 1.08 for the BGO detector and G3 was 1.07 for the LSO. A value of almost unity for G2 of the LSO detector indicated a nonsignificant optimization by altering the energy window setting. G' was found to be ∼1.4 times higher for the TOF-permitting detector after reconstruction and optimization of the coincidence and energy windows. The method described could potentially predict image noise variations by altering detector acquisition parameters. It could also further contribute toward a long-lasting debate related to cost-efficiency issues of TOF scanners versus the non-TOF ones. Some vendors re-engage nowadays to non-TOF product line designs in an effort to reduce crystal costs. Therefore, exploring the limits of image quality gain by altering the parameters of these detectors remains a topical issue.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogunovic, Hrvoje; Pozo, Jose Maria; Villa-Uriol, Maria Cruz

Purpose: To evaluate the suitability of an improved version of an automatic segmentation method based on geodesic active regions (GAR) for segmenting cerebral vasculature with aneurysms from 3D x-ray reconstruction angiography (3DRA) and time of flight magnetic resonance angiography (TOF-MRA) images available in the clinical routine. Methods: Three aspects of the GAR method have been improved: execution time, robustness to variability in imaging protocols, and robustness to variability in image spatial resolutions. The improved GAR was retrospectively evaluated on images from patients containing intracranial aneurysms in the area of the Circle of Willis and imaged with two modalities: 3DRA andmore » TOF-MRA. Images were obtained from two clinical centers, each using different imaging equipment. Evaluation included qualitative and quantitative analyses of the segmentation results on 20 images from 10 patients. The gold standard was built from 660 cross-sections (33 per image) of vessels and aneurysms, manually measured by interventional neuroradiologists. GAR has also been compared to an interactive segmentation method: isointensity surface extraction (ISE). In addition, since patients had been imaged with the two modalities, we performed an intermodality agreement analysis with respect to both the manual measurements and each of the two segmentation methods. Results: Both GAR and ISE differed from the gold standard within acceptable limits compared to the imaging resolution. GAR (ISE) had an average accuracy of 0.20 (0.24) mm for 3DRA and 0.27 (0.30) mm for TOF-MRA, and had a repeatability of 0.05 (0.20) mm. Compared to ISE, GAR had a lower qualitative error in the vessel region and a lower quantitative error in the aneurysm region. The repeatability of GAR was superior to manual measurements and ISE. The intermodality agreement was similar between GAR and the manual measurements. Conclusions: The improved GAR method outperformed ISE qualitatively as well as quantitatively and is suitable for segmenting 3DRA and TOF-MRA images from clinical routine.« less

MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories.

PubMed

Tracz, Dobryan M; Tober, Ashley D; Antonation, Kym S; Corbett, Cindi R

2018-03-01

We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.

Effect of time-of-flight and point spread function modeling on detectability of myocardial defects in PET

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefferkoetter, Joshua, E-mail: dnrjds@nus.edu.sg; Ouyang, Jinsong; Rakvongthai, Yothin

2014-06-15

Purpose: A study was designed to investigate the impact of time-of-flight (TOF) and point spread function (PSF) modeling on the detectability of myocardial defects. Methods: Clinical FDG-PET data were used to generate populations of defect-present and defect-absent images. Defects were incorporated at three contrast levels, and images were reconstructed by ordered subset expectation maximization (OSEM) iterative methods including ordinary Poisson, alone and with PSF, TOF, and PSF+TOF. Channelized Hotelling observer signal-to-noise ratio (SNR) was the surrogate for human observer performance. Results: For three iterations, 12 subsets, and no postreconstruction smoothing, TOF improved overall defect detection SNR by 8.6% as comparedmore » to its non-TOF counterpart for all the defect contrasts. Due to the slow convergence of PSF reconstruction, PSF yielded 4.4% less SNR than non-PSF. For reconstruction parameters (iteration number and postreconstruction smoothing kernel size) optimizing observer SNR, PSF showed larger improvement for faint defects. The combination of TOF and PSF improved mean detection SNR as compared to non-TOF and non-PSF counterparts by 3.0% and 3.2%, respectively. Conclusions: For typical reconstruction protocol used in clinical practice, i.e., less than five iterations, TOF improved defect detectability. In contrast, PSF generally yielded less detectability. For large number of iterations, TOF+PSF yields the best observer performance.« less

Utilization of matrix-assisted laser desorption and ionization time-of-flight mass spectrometry for identification of infantile seborrheic dermatitis-causing Malassezia and incidence of culture-based cutaneous Malassezia microbiota of 1-month-old infants.

PubMed

Yamamoto, Mikachi; Umeda, Yoshiko; Yo, Ayaka; Yamaura, Mariko; Makimura, Koichi

2014-02-01

Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been utilized for identification of various microorganisms. Malassezia species, including Malassezia restricta, which is associated with seborrheic dermatitis, has been difficult to identify by traditional means. This study was performed to develop a system for identification of Malassezia species with MALDI-TOF-MS and to investigate the incidence and variety of cutaneous Malassezia microbiota of 1-month-old infants using this technique. A Malassezia species-specific MALDI-TOF-MS database was developed from eight standard strains, and the availability of this system was assessed using 54 clinical strains isolated from the skin of 1-month-old infants. Clinical isolates were cultured initially on CHROMagar Malassezia growth medium, and the 28S ribosomal DNA (D1/D2) sequence was analyzed for confirmatory identification. Using this database, we detected and analyzed Malassezia species in 68% and 44% of infants with and without infantile seborrheic dermatitis, respectively. The results of MALDI-TOF-MS analysis were consistent with those of rDNA sequencing identification (100% accuracy rate). To our knowledge, this is the first report of a MALDI-TOF-MS database for major skin pathogenic Malassezia species. This system is an easy, rapid and reliable method for identification of Malassezia. © 2014 Japanese Dermatological Association.

Energy discrimination for positron emission tomography using the time information of the first detected photons

NASA Astrophysics Data System (ADS)

Therrien, A. C.; Lemaire, W.; Lecoq, P.; Fontaine, R.; Pratte, J.-F.

2018-01-01

The advantages of Time-of-Flight positron emission tomography (TOF-PET) have pushed the development of detectors with better time resolution. In particular, Silicon Photomultipliers (SiPM) have evolved tremendously in the past decade and arrays with a fully digital readout are the next logical step (dSiPM). New multi-timestamp methods use the precise time information of multiple photons to estimate the time of a PET event with greater accuracy, resulting in excellent time resolution. We propose a method which uses the same timestamps as the time estimator to perform energy discrimination, thus using data obtained within 5 ns of the beginning of the event. Having collected all the necessary information, the dSiPM could then be disabled for the remaining scintillation while dedicated electronics process the collected data. This would reduce afterpulsing as the SPAD would be turned off for several hundred nanoseconds, emptying the majority of traps. The proposed method uses a strategy based on subtraction and minimal electronics to reject energy below a selected threshold. This method achieves an error rate of less than 3% for photopeak discrimination (threshold at 400 keV) for dark count rates up to 100 cps/μm2, time-to-digital converter resolution up to 50 ps and a photon detection efficiency ranging from 10 to 70%.

Encrypted Three-dimensional Dynamic Imaging using Snapshot Time-of-flight Compressed Ultrafast Photography

PubMed Central

Liang, Jinyang; Gao, Liang; Hai, Pengfei; Li, Chiye; Wang, Lihong V.

2015-01-01

Compressed ultrafast photography (CUP), a computational imaging technique, is synchronized with short-pulsed laser illumination to enable dynamic three-dimensional (3D) imaging. By leveraging the time-of-flight (ToF) information of pulsed light backscattered by the object, ToF-CUP can reconstruct a volumetric image from a single camera snapshot. In addition, the approach unites the encryption of depth data with the compressed acquisition of 3D data in a single snapshot measurement, thereby allowing efficient and secure data storage and transmission. We demonstrated high-speed 3D videography of moving objects at up to 75 volumes per second. The ToF-CUP camera was applied to track the 3D position of a live comet goldfish. We have also imaged a moving object obscured by a scattering medium. PMID:26503834

Corona discharge ion mobility spectrometry with orthogonal acceleration time of flight mass spectrometry for monitoring of volatile organic compounds.

PubMed

Sabo, Martin; Matejčík, Štefan

2012-06-19

We demonstrate the application of corona discharge ion mobility spectrometry with orthogonal acceleration time of flight mass spectrometry (CD IMS-oaTOF) for volatile organic compounds (VOCs) monitoring. Two-dimensional (2D) IMS-oaTOF spectra of VOCs were recorded in nearly real time. The corona discharge atmospheric pressure chemical ionization (APCI) source was operated in positive mode in nitrogen and air. The CD ion source generates in air H(3)O(+)(H(2)O)(n) and NO(+). The NO(+) offers additional possibility for selective ionization and for an increase of the sensitivity of monoaromatic compounds. In addition to H(3)O(+)(H(2)O)(n) and NO(+), we have carried out ionization of VOCs using acetone as dopant gas ((CH(3))(2)COH(+)). Sixteen model VOCs (tetrahydrofuran, butanol, n-propanol, iso-propano, acetone, methanol, ethanol, toluene, benzene, amomnia, dioxan, triethylamine, acetonitrile, formaldehyde, m-xylene, 2,2,2-trifluoroethylamine) were tested using these ionization techniques.

High mass resolution, high angular acceptance time-of-flight mass spectroscopy for planetary missions under the Planetary Instrument Definition and Development Program (PIDDP)

NASA Technical Reports Server (NTRS)

Young, David T.

1991-01-01

This final report covers three years and several phases of work in which instrumentation for the Planetary Instrument Definition and Development Program (PIDDP) were successfully developed. There were two main thrusts to this research: (1) to develop and test methods for electrostatically scanning detector field-of-views, and (2) to improve the mass resolution of plasma mass spectrometers to M/delta M approximately 25, their field-of-view (FOV) to 360 degrees, and their E-range to cover approximately 1 eV to 50 keV. Prototypes of two different approaches to electrostatic scanning were built and tested. The Isochronous time-of-flight (TOF) and the linear electric field 3D TOF devices were examined.

High-energy and low-energy collision-induced dissociation of protonated flavonoids generated by MALDI and by electrospray ionization

NASA Astrophysics Data System (ADS)

March, Raymond E.; Li, Hongxia; Belgacem, Omar; Papanastasiou, Dimitris

2007-04-01

Product ion mass spectra of a series of nine protonated flavonoids have been observed by electrospray ionization combined with quadrupole/time-of-flight (ESI QTOF), and matrix-assisted laser desorption ionization combined either with quadrupole ion trap (MALDI QIT) tandem mass spectrometry or time-of-flight tandem mass spectrometry (MALDI TOF ReTOF). The compounds examined are 3,6-, 3,2'-, and 3,3'-dihydoxyflavone, apigenin (5,7,4'-trihydroxyflavone), luteolin (5,7,3',4'-tetrahydroxyflavone), apigenin-7-O-glucoside, hesperidin (5,7,3'-trihydroxy-4'-methoxyflavanone), daidzen (7,4'-dihydroxyisoflavone), and rutin (quercitin-3-O-rutinoside) where quercitin is 3,5,7,3',4'-pentahydroxyflavone; sodiated rutin was examined also. The center-of-mass energies in ESI QTOF and MALDI QIT are similar (1-4 eV) and their product ion mass spectra are virtually identical. In the MALDI TOF ReTOF instrument, center-of-mass energies range from 126-309 eV for sodiated rutin to protonated dihydroxyflavones, respectively. Due to the high center-of-mass energies available with the MALDI TOF ReTOF instrument, some useful structural information may be obtained; however, with increasing precursor mass/charge ratio, product ion mass spectra become simplified so as to be of limited structural value. Electronic excitation of the protonated (and sodiated) species examined here offers an explanation for the very simple product ion mass spectra observed particularly for glycosylated flavonoids.

Proteomic analysis of intestinal tissues from mice fed with Lentinula edodes-derived polysaccharides.

PubMed

Xu, Xiaofei; Yang, Jiguo; Ning, Zhengxiang; Zhang, Xuewu

2016-01-01

Lentinula edodes-derived polysaccharides are well known for their immunomodulation and antitumor activities. However, the mechanisms of action have not been fully elucidated. This study presents proteomic analysis of the colon and small intestine from mice fed with an immunostimulating heteropolysaccharide L2 from the fruit body of L. edodes. Two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF MS/MS were employed to characterize the protein profiles. Twenty nine gel spots representing 20 proteins in colon tissues and 38 gel spots in small intestine tissues representing 23 proteins were identified as showing significant changes in abundance. These differential proteins in abundance are mainly involved in metabolism, binding, structural components, and response to stimulus. Protein-protein interaction network analysis demonstrated mapping of the 20 colon proteins to a 7-protein and a 3-protein sub-network, and mapping of the 23 small intestine proteins to a 9-protein and a 5-protein sub-network. All the 40 altered proteins were integrated into a unified network containing 25 proteins, suggesting the existence of a concerted mechanism, although acting on the colon and small intestine separately. These findings facilitate the understanding of the regulatory mechanism in response to L2 treatment.

Conotruncal anomalies in the fetus: Referral patterns and pregnancy outcomes in a dedicated fetal cardiology unit in South India.

PubMed

Vaidyanathan, Balu; Kumar, Shine; Sudhakar, Abish; Kumar, Raman Krishna

2013-01-01

To describe the referral patterns and pregnancy outcomes of fetuses with conotruncal anomalies (CTA) from a fetal cardiology unit in South India. Records of 68 women identified to have diagnosis of CTA on fetal echocardiography (mean gestational age 26.8 ± 5.9 weeks; range 17-38 weeks) during the period 2008-2011 were reviewed. The most common indication for referral was suspected congenital heart disease during routine antenatal scan (89.7%). The various CTA diagnosed included Tetralogy of Fallot (TOF, 44.1%), Double outlet right ventricle (DORV, 27.9%), Transposition of great vessels (TGA, 8.8%), TOF with pulmonary atresia (TOF-PA, 8.8%), TOF absent pulmonary valve (TOF-APV, 7.4%) and truncus arteriosus (TA, 2.9%). Extra cardiac anomalies were reported in 4 fetuses (7.1%). Pregnancy outcomes included pregnancies not culminating in live-birth (54.4%), delivery at term (41.2%) with 3 patients (4.4%) being lost to follow-up. Proportion of pregnancies not culminating in live-birth lesion wise include: TOF (53.3%), DORV (52.6%), TGA (50%), TOF -APV (80%), TOF-PA (50%), and TA (50%). Twenty-four babies (35.3%) received post-natal cardiac care with 5 (7.4%) undergoing neonatal surgical procedures. Seven babies (10.3%) died in neonatal period, including 2 who underwent surgery. The accuracy of fetal echo was 96.4% for primary lesion and 67.9% for complete segmental diagnosis. Pre-natal diagnosis of CTA, despite a high diagnostic accuracy, prompted utilization of post-natal tertiary cardiac care in a limited proportion of patients, including those with reparable lesions. Focus in developing countries should shift towards earlier referral, improving awareness about treatment options and a comprehensive evaluation for associated anomalies.

Identification of proteins in a human pleural exudate using two-dimensional preparative liquid-phase electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Nilsson, C L; Puchades, M; Westman, A; Blennow, K; Davidsson, P

1999-01-01

Pleural effusion may occur in patients suffering from physical trauma or systemic disorders such as infection, inflammation, or cancer. In order to investigate proteins in a pleural exudate from a patient with severe pneumonia, we used a strategy that combined preparative two-dimensional liquid-phase electrophoresis (2-D LPE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and Western blotting. Preparative 2-D LPE is based on the same principles as analytical 2-D gel electrophoresis, except that the proteins remain in liquid phase during the entire procedure. In the first dimension, liquid-phase isoelectric focusing allows for the enrichment of proteins in liquid fractions. In the Rotofor cell, large volumes (up to 55 mL) and protein amounts (up to 1-2 g) can be loaded. Several low abundance proteins, cystatin C, haptoglobin, transthyretin, beta2-microglobulin, and transferrin, were detected after liquid-phase isoelectric focusing, through Western blotting analysis, in a pleural exudate (by definition, >25 g/L total protein). Direct MALDI-TOF-MS analysis of proteins in a Rotofor fraction is demonstrated as well. MALDI-TOF-MS analysis of a tryptic digest of a continuous elution sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) fraction confirmed the presence of cystatin C. By applying 2-D LPE, MALDI-TOF-MS, and Western blotting to the analysis of this pleural exudate, we were able to confirm the identity of proteins of potential diagnostic value. Our findings serve to illustrate the usefulness of this combination of methods in the analysis of pathological fluids.

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS.

PubMed

Davies, Sarah K; Fearn, Sarah; Allsopp, Luke P; Harrison, Freya; Ware, Ecaterina; Diggle, Stephen P; Filloux, Alain; McPhail, David S; Bundy, Jacob G

2017-01-01

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight-secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples-both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.

Non-enhanced MR imaging of cerebral aneurysms: 7 Tesla versus 1.5 Tesla.

PubMed

Wrede, Karsten H; Dammann, Philipp; Mönninghoff, Christoph; Johst, Sören; Maderwald, Stefan; Sandalcioglu, I Erol; Müller, Oliver; Özkan, Neriman; Ladd, Mark E; Forsting, Michael; Schlamann, Marc U; Sure, Ulrich; Umutlu, Lale

2014-01-01

To prospectively evaluate 7 Tesla time-of-flight (TOF) magnetic resonance angiography (MRA) in comparison to 1.5 Tesla TOF MRA and 7 Tesla non-contrast enhanced magnetization-prepared rapid acquisition gradient-echo (MPRAGE) for delineation of unruptured intracranial aneurysms (UIA). Sixteen neurosurgical patients (male n = 5, female n = 11) with single or multiple UIA were enrolled in this trial. All patients were accordingly examined at 7 Tesla and 1.5 Tesla MRI utilizing dedicated head coils. The following sequences were obtained: 7 Tesla TOF MRA, 1.5 Tesla TOF MRA and 7 Tesla non-contrast enhanced MPRAGE. Image analysis was performed by two radiologists with regard to delineation of aneurysm features (dome, neck, parent vessel), presence of artifacts, vessel-tissue-contrast and overall image quality. Interobserver accordance and intermethod comparisons were calculated by kappa coefficient and Lin's concordance correlation coefficient. A total of 20 intracranial aneurysms were detected in 16 patients, with two patients showing multiple aneurysms (n = 2, n = 4). Out of 20 intracranial aneurysms, 14 aneurysms were located in the anterior circulation and 6 aneurysms in the posterior circulation. 7 Tesla MPRAGE imaging was superior over 1.5 and 7 Tesla TOF MRA in the assessment of all considered aneurysm and image quality features (e.g. image quality: mean MPRAGE7T: 5.0; mean TOF7T: 4.3; mean TOF1.5T: 4.3). Ratings for 7 Tesla TOF MRA were equal or higher over 1.5 Tesla TOF MRA for all assessed features except for artifact delineation (mean TOF7T: 4.3; mean TOF1.5T 4.4). Interobserver accordance was good to excellent for most ratings. 7 Tesla MPRAGE imaging demonstrated its superiority in the detection and assessment of UIA as well as overall imaging features, offering excellent interobserver accordance and highest scores for all ratings. Hence, it may bear the potential to serve as a high-quality diagnostic tool for pretherapeutic assessment and follow-up of untreated UIA.

Non-Enhanced MR Imaging of Cerebral Aneurysms: 7 Tesla versus 1.5 Tesla

PubMed Central

Wrede, Karsten H.; Dammann, Philipp; Mönninghoff, Christoph; Johst, Sören; Maderwald, Stefan; Sandalcioglu, I. Erol; Müller, Oliver; Özkan, Neriman; Ladd, Mark E.; Forsting, Michael; Schlamann, Marc U.; Sure, Ulrich; Umutlu, Lale

2014-01-01

Purpose To prospectively evaluate 7 Tesla time-of-flight (TOF) magnetic resonance angiography (MRA) in comparison to 1.5 Tesla TOF MRA and 7 Tesla non-contrast enhanced magnetization-prepared rapid acquisition gradient-echo (MPRAGE) for delineation of unruptured intracranial aneurysms (UIA). Material and Methods Sixteen neurosurgical patients (male n = 5, female n = 11) with single or multiple UIA were enrolled in this trial. All patients were accordingly examined at 7 Tesla and 1.5 Tesla MRI utilizing dedicated head coils. The following sequences were obtained: 7 Tesla TOF MRA, 1.5 Tesla TOF MRA and 7 Tesla non-contrast enhanced MPRAGE. Image analysis was performed by two radiologists with regard to delineation of aneurysm features (dome, neck, parent vessel), presence of artifacts, vessel-tissue-contrast and overall image quality. Interobserver accordance and intermethod comparisons were calculated by kappa coefficient and Lin's concordance correlation coefficient. Results A total of 20 intracranial aneurysms were detected in 16 patients, with two patients showing multiple aneurysms (n = 2, n = 4). Out of 20 intracranial aneurysms, 14 aneurysms were located in the anterior circulation and 6 aneurysms in the posterior circulation. 7 Tesla MPRAGE imaging was superior over 1.5 and 7 Tesla TOF MRA in the assessment of all considered aneurysm and image quality features (e.g. image quality: mean MPRAGE7T: 5.0; mean TOF7T: 4.3; mean TOF1.5T: 4.3). Ratings for 7 Tesla TOF MRA were equal or higher over 1.5 Tesla TOF MRA for all assessed features except for artifact delineation (mean TOF7T: 4.3; mean TOF1.5T 4.4). Interobserver accordance was good to excellent for most ratings. Conclusion 7 Tesla MPRAGE imaging demonstrated its superiority in the detection and assessment of UIA as well as overall imaging features, offering excellent interobserver accordance and highest scores for all ratings. Hence, it may bear the potential to serve as a high-quality diagnostic tool for pretherapeutic assessment and follow-up of untreated UIA. PMID:24400100

(1→3)-β-d-Glucan oligosaccharides monomers purification and its H2O2 induction effect study.

PubMed

Fu, Yunbin; Wang, Mengyu; Wang, Wenxia; Tuo, Yaqin; Guo, Zhimou; Du, Yuguang; Yin, Heng

2015-11-01

In order to produce highly purified (1→3)-β-d-glucan oligosaccharides ((1→3)-β-d-GOS) monomers, a hydrophilic interaction liquid chromatography (HILIC) system with X-Amide stationary phase was performed. Nine (1→3)-β-d-GOS monomers with degree of polymerization (DP) from 2 to 10 were successfully separated. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) demonstrated that these monomers were with high purity. Furthermore, a hydrogen peroxide (H2O2) online detection method was established to monitor H2O2 releases in tobacco cells. This is the first report on nine consecutive (1→3)-β-d-GOS monomers purification and its effect upon H2O2-releasing in plants. It was found that (1→3)-β-d-GOS monomers with higher DP induced stronger defense responses in plants, which will pave the way for elucidating the relationship between (1→3)-β-d-GOS and biological activities. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis, Spectral and Photophysical Properties of Anthracene Substituted Phthalocyanines; A Study as Polyurethane Electrospun Nanofibers.

PubMed

Ku, Kyo-Sun; Kumar, Rangaraju Satish; Son, Young-A

2018-03-01

We have designed and synthesized novel symmetrical anthracene substituted zinc(II), copper(II), cobalt(II) and nickel(II) phthalocyanines (PC1, PC2, PC3 and PC4) in this work. For this synthesis, we started from base-catalysed aromatic displacement reaction of 4-nitrophthalonitrile with 9-hydroxyanthracene. The resulting four phthalocyanines (PCs) have been fully characterized by a series of spectroscopic methods including electronic absorption, elemental analysis, MALDI-TOF mass, and IR spectroscopy. The aggregation behavior of these PCs was investigated in different concentrations of chloroform solution. Further thermal stability also investigated by TG analysis. Finally we successfully made phthalocyanine (PC1) blended polyurethane electrospun (ES) nanofibers.

In-beam test of the RPC architecture foreseen to be used for the CBM-TOF inner wall

NASA Astrophysics Data System (ADS)

Petriş, M.; Bartoş, D.; Petrovici, M.; Rădulescu, L.; Simion, V.; Deppner, I.; Herrmann, N.; Simon, C.; Frühauf, J.; Kiš, M.; Loizeau, P.-A.

2018-05-01

The Time Of Flight (TOF) subsystem is one of the main detectors of the CBM experiment. The TOF wall in conjunction with Silicon Tracking System (STS) is foreseen to identify charged hadrons, i.e. pions, kaons and protons, with a full azimuthal coverage at 2.50 - 250 polar angles. A system time resolution of at least 80 ps, including all contributions, such as electronics jitter and the resolution of the time reference system, is required. Such a performance should be maintained up to a counting rate larger than 30 kHz/cm2 at the most inner region of TOF wall. Our R&D activity has been focused on the development of two-dimensional position sensitive Multi-gap Resistive Plate Counter (MRPC) prototypes for the forward region of the CBM-TOF subdetector, the most demanding zone in terms of granularity and counting rate. The in-beam tests using secondary particles produced in 30 GeV/u Pb ion collisions on a Pb target at SPS - CERN aimed to test the performance of these prototypes in conditions similar to the ones expected at SIS100 at FAIR. The performance of the prototypes is studied in conditions of exposure of the whole active area of the chamber to high multiplicity of reaction products. The results show that this type of MRPC fulfill the challenging requirements of the CBM-TOF wall. Therefore, such an architecture is recommended as basic solution for CBM-TOF inner zone.

Dynamics of the reaction of atomic oxygen with ethene: Observation of all carbon-containing products by single-photon ionization

NASA Astrophysics Data System (ADS)

Lee, Shih-Huang; Huang, Wen-Jian; Chen, Wei-Kan

2007-10-01

We measured time-of-flight (TOF) spectra of products from the reaction O( 3P/ 1D) + C 2H 4 at collision energy 6.4 kcal mol -1 using a quadrupole mass filter and tunable vacuum-ultraviolet light for ionization. All carbon-containing products from five exit channels - CH 2CHO + H, CH 2CO + H 2, CH 3 + HCO, CH 2 + HCHO, and CH 2CO + 2H - were identified. Product channels CH 2CHO + H and CH 2CO + 2H associate with 3P and 1D atomic oxygen reactants, respectively. Both 3P and 1D oxygen reactants might be responsible for the other reactions. The ionization threshold of nascent vinoxy radicals is 9.3 ± 0.1 eV.

Non-ECG-gated unenhanced MRA of the carotids: optimization and clinical feasibility.

PubMed

Raoult, H; Gauvrit, J Y; Schmitt, P; Le Couls, V; Bannier, E

2013-11-01

To optimise and assess the clinical feasibility of a carotid non-ECG-gated unenhanced MRA sequence. Sixteen healthy volunteers and 11 patients presenting with internal carotid artery (ICA) disease underwent large field-of-view balanced steady-state free precession (bSSFP) unenhanced MRA at 3T. Sampling schemes acquiring the k-space centre either early (kCE) or late (kCL) in the acquisition window were evaluated. Signal and image quality was scored in comparison to ECG-gated kCE unenhanced MRA and TOF. For patients, computed tomography angiography was used as the reference. In volunteers, kCE sampling yielded higher image quality than kCL and TOF, with fewer flow artefacts and improved signal homogeneity. kCE unenhanced MRA image quality was higher without ECG-gating. Arterial signal and artery/vein contrast were higher with both bSSFP sampling schemes than with TOF. The kCE sequence allowed correct quantification of ten significant stenoses, and it facilitated the identification of an infrapetrous dysplasia, which was outside of the TOF imaging coverage. Non-ECG-gated bSSFP carotid imaging offers high-quality images and is a promising sequence for carotid disease diagnosis in a short acquisition time with high spatial resolution and a large field of view. • Non-ECG-gated unenhanced bSSFP MRA offers high-quality imaging of the carotid arteries. • Sequences using early acquisition of the k-space centre achieve higher image quality. • Non-ECG-gated unenhanced bSSFP MRA allows quantification of significant carotid stenosis. • Short MR acquisition times and ungated sequences are helpful in clinical practice. • High 3D spatial resolution and a large field of view improve diagnostic performance.

Accessing the Nitromethane (CH3NO2) Potential Energy Surface in Methanol (CH3OH)-Nitrogen Monoxide (NO) Ices Exposed to Ionizing Radiation: An FTIR and PI-ReTOF-MS Investigation.

PubMed

Góbi, Sándor; Crandall, Parker B; Maksyutenko, Pavlo; Förstel, Marko; Kaiser, Ralf I

2018-03-08

(D 3 -)Methanol-nitrogen monoxide (CH 3 OH/CD 3 OH-NO) ices were exposed to ionizing radiation to facilitate the eventual determination of the CH 3 NO 2 potential energy surface (PES) in the condensed phase. Reaction intermediates and products were monitored via infrared spectroscopy (FTIR) and photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS) during the irradiation and temperature controlled desorption (TPD) phase, respectively. Distinct photoionization energies were utilized to discriminate the isomer(s) formed in these processes. The primary methanol radiolysis products were the methoxy (CH 3 O) and hydroxymethyl (CH 2 OH) radicals along with atomic hydrogen. The former was found to react barrierlessly with nitrogen monoxide resulting in the formation of cis- and trans-methyl nitrite (CH 3 ONO), which is the most abundant product that can be observed in the irradiated samples. On the other hand, the self-recombination of hydroxymethyl radicals yielding ethylene glycol (HO(CH 2 ) 2 OH) and glycerol (HOCH 2 CH 2 (OH)CH 2 OH) is preferred over the recombination with nitrogen monoxide to nitrosomethanol (HOCH 2 NO).

Testing of Front End Electronics for 10ps Time of Flight Detectors

NASA Astrophysics Data System (ADS)

Kimball, Matthew; EIC PID Consortium Collaboration

2016-09-01

To fully achieve the physics goals of the future Electron Ion Collider (EIC), continued development of the detectors involved is needed. One area of research involves improving the timing resolution of Time of Flight (ToF) detectors from 100ps to 10ps. When the timing resolution of these ToF detectors is improved, better particle identification can be achieved. In addition, as ToF detectors are being constructed with ever improving timing resolution, the need to improve the high speed performance of the fast electronics used in their front-end electronics (FEE) increases. A series of careful measurements has been performed to investigate the performance and efficiency of each element in the FEE chain. The focus of these tests lies on the amplitude transmission efficiency of the high speed signals as a function of frequency, also known as the bandwidth. The components tested include balanced to unbalanced (balun) boards, signal pre-amps, and waveform digitizers. These tests were performed on individual components and with all elements connected over a frequency range of 1MHz to 1GHz. The results of these tests will be presented. This research was supported by US DOE MENP Grant DE-FG02-03ER41243.

ToF diagnostic of Tin resonant laser photoionization in SPES laser offline laboratory

NASA Astrophysics Data System (ADS)

Scarpa, D.; Fedorov, D.; Andrighetto, A.; Mariotti, E.; Nicolosi, P.; Sottili, L.; Tomaselli, A.; Cecchi, R.; Stiaccini, L.

2016-09-01

Tin is the principal element of interest in the SPES ISOL facility, which is under construction at Legnaro INFN Laboratories. Atomic nuclei have a shell structure in which nuclei with \\textquoteleft magic numbers\\textquoteright of protons and neutrons are analogous to the noble gasses in atomic physics. In particular, recent theoretical studies, reveal double-magic nature of radioactive 132Sn. For this reason the nuclear physics community demonstrated, in the last years, a huge interest to produce and study this radioactive neutron rich isotope. Experiments on Tin laser resonant ionization have been performed in the offline SPES laser laboratory to investigate the capability of the new home-made Time of Flight (ToF) mass spectrometer. Several three-step, two color ionization schemes have been tested by comparing fast and slow optogalvanic signals from a Tin Hollow Cathode Lamp (HCL) and Time of Flight signals from the spectrometer. By scanning the wavelength of one of the two dye lasers across the specific resonance, comparisons of ionization signals from both the ToF and the HCL have been made, finding perfect agreement. Furthermore, with the mass spectrometer, resolved peaks of all the natural Tin isotopes have been detected. The natural abundances extracted from these measurements are in agreement with the table values for Tin isotopes. This work, with comparison of OGE and ToF signals, confirm the fully functional SPES offline laser laboratory capability in order to develop scheme studies also for the other possible Radioactive Ion Beam (RIB) elements.

Rapid, sensitive and simultaneous determination of fluorescence-labeled polyamines in human hair by high-pressure liquid chromatography coupled with electrospray-ionization time-of-flight mass spectrometry.

PubMed

Sugiura, Koichi; Min, Jun Zhe; Toyo'oka, Toshimasa; Inagaki, Shinsuke

2008-09-26

The rapid, sensitive and simultaneous determination of six polyamines, i.e., ornithine (ORN), 1,3-diaminopropane (DAP), putrescine (PUT), cadaverine (CAD), spermidine (SPD) and spermine (SPM), in human hairs was performed by ultra-performance liquid chromatography (UPLC) with fluorescence (FL) detection and electrospray-ionization time-of-flight mass spectrometry (ESI-TOF-MS). The primary (-NH(2)) and secondary (-NH) amines in the polyamine structures were first labeled with 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F) at 60 degrees C for 30 min in the mixture of 0.1M borax (pH 9.3) and acetonitrile (CH(3)CN). The resulting derivatives were perfectly separated using an ACQUITY UPLC BEH C(18) column (1.7 microm, 100 mm x 2.1mm i.d.) by a gradient elution with a mixture of water-acetonitrile containing 0.1% formic acid (HCOOH). The separated polyamine derivatives were sensitively detected with both FL and TOF-MS. The detection limits in FL and TOF-MS were 11-86 and 2-5 fmol, respectively. However, the determination of several polyamines by FL detection was interfered with by endogenous substances in the hair. Therefore, the simultaneous determination in hair was carried out by the combination of UPLC separation and the ESI-TOF-MS detection. The structures of the polyamines were identified from the protonated-molecular ions [M+H](+) obtained from the TOF-MS measurement. A good linearity was achieved from the calibration curves, that was obtained by plotting the peak area ratios of the analytes relative to the internal standard (IS), i.e., 1,6-diaminohexane (DAH), against the injected amounts of each polyamine (0.05-50 pmol, r(2)>0.999). The proposed method was applied to the determination in the hairs of healthy volunteers. The mean concentrations of ORN, DAP, PUT, CAD, SPD and SPM in 1mg of human hairs (n=20) were 1.46, 0.18, 1.18, 0.11, 1.97 and 0.98 pmol, respectively. Because the proposed method provides a good mass accuracy and the trace detection of the polyamines in hair, this analytical technique seems to be applicable for the determination of various biological compounds in hair.

Timing resolution studies of the optical part of the AFP Time-of-flight detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chytka, L.; Avoni, G.; Brandt, A.

We present results of the timing performance studies of the optical part and front-end electronics of the time-of-flight subdetector prototype for the ATLAS Forward Proton (AFP) detector obtained during the test campaigns at the CERN-SPS test-beam facility (120 GeV π + particles) in July 2016 and October 2016. The time-of-flight (ToF) detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgroundsmore » that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from the ToF allows the proton tagger to operate at the high luminosity required for the measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through them. The emitted Cherenkov photons are detected by a multi-anode micro-channel plate photomultiplier tube (MCP-PMT) and processed by fast electronics.« less

Characterization of constituents in Stellera chamaejasme L. by rapid-resolution liquid chromatography-diode array detection and electrospray ionization time-of-flight mass spectrometry.

PubMed

Zhao, Liang; Lou, Zi-Yang; Zhu, Zhen-Yu; Zhang, Guo-Qing; Chai, Yi-Feng

2008-01-01

A reliable and rapid method based on rapid-resolution liquid chromatography-diode array detection (RRLC-DAD) and electrospray ionization time-of-flight mass spectrometry (ESI-TOF/MS) has been developed for the isolation and characterization of multiple constituents in the root of Stellera chamaejasme L., which was extracted by sonication with methanol in an optimized procedure. Separation of the multiple constituents was achieved on an Agilent Zorbax XDB-C18 (50x3.0 mm i.d.; 1.8 microm) column using a gradient elution at a flow rate of 0.4 mL/min. The detection wavelength was 210 nm. Mass spectra were acquired in both positive and negative modes. A formula database of the known chemical constituents in the root of Stellera chamaejasme L. was established by an Agilent software. Twenty-two obvious peaks appeared in the total ion chromatogram and nine of them were characterized by TOF/MS. The RRLC-DAD and ESI-TOF/MS method with ultrasonic extraction would be useful for rapid and effective characterization of chemical constituents in the root of Stellera chamaejasme L. Copyright (c) 2007 John Wiley & Sons, Ltd.

Timing resolution studies of the optical part of the AFP Time-of-flight detector

DOE PAGES

Chytka, L.; Avoni, G.; Brandt, A.; ...

2018-04-02

We present results of the timing performance studies of the optical part and front-end electronics of the time-of-flight subdetector prototype for the ATLAS Forward Proton (AFP) detector obtained during the test campaigns at the CERN-SPS test-beam facility (120 GeV π + particles) in July 2016 and October 2016. The time-of-flight (ToF) detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgroundsmore » that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from the ToF allows the proton tagger to operate at the high luminosity required for the measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through them. The emitted Cherenkov photons are detected by a multi-anode micro-channel plate photomultiplier tube (MCP-PMT) and processed by fast electronics.« less

Fully automated two-step assay for detection of metallothionein through magnetic isolation using functionalized γ-Fe2O3 particles.

PubMed

Merlos Rodrigo, Miguel Angel; Krejcova, Ludmila; Kudr, Jiri; Cernei, Natalia; Kopel, Pavel; Richtera, Lukas; Moulick, Amitava; Hynek, David; Adam, Vojtech; Stiborova, Marie; Eckschlager, Tomas; Heger, Zbynek; Zitka, Ondrej

2016-12-15

Metallothioneins (MTs) are involved in heavy metal detoxification in a wide range of living organisms. Currently, it is well known that MTs play substantial role in many pathophysiological processes, including carcinogenesis, and they can serve as diagnostic biomarkers. In order to increase the applicability of MT in cancer diagnostics, an easy-to-use and rapid method for its detection is required. Hence, the aim of this study was to develop a fully automated and high-throughput assay for the estimation of MT levels. Here, we report the optimal conditions for the isolation of MTs from rabbit liver and their characterization using MALDI-TOF MS. In addition, we described a two-step assay, which started with an isolation of the protein using functionalized paramagnetic particles and finished with their electrochemical analysis. The designed easy-to-use, cost-effective, error-free and fully automated procedure for the isolation of MT coupled with a simple analytical detection method can provide a prototype for the construction of a diagnostic instrument, which would be appropriate for the monitoring of carcinogenesis or MT-related chemoresistance of tumors. Copyright © 2016 Elsevier B.V. All rights reserved.

3D Perception Technologies for Surgical Operating Theatres.

PubMed

Beyl, T; Schreiter, L; Nicolai, P; Raczkowsky, J; Wörn, H

2016-01-01

3D Perception technologies have been explored in various fields. This paper explores the application of such technologies for surgical operating theatres. Clinical applications can be found in workflow detection, tracking and analysis, collision avoidance with medical robots, perception of interaction between participants of the operation, training of the operation room crew, patient calibration and many more. In this paper a complete perception solution for the operating room is shown. The system is based on the ToF technology integrated to the Microsoft Kinect One implements a multi camera approach. Special emphasize is put on the tracking of the personnel and the evaluation of the system performance and accuracy.

Characterizing ICF Neutron Scintillation Diagnostics on the nTOF line at SUNY Geneseo

NASA Astrophysics Data System (ADS)

Lawson-Keister, Pat; Padawar-Curry, Jonah; Visca, Hannah; Fletcher, Kurt; Padalino, Stephen; Sangster, T. Craig; Regan, Sean

2015-11-01

Neutron scintillator diagnostics for ICF and HEDP can be characterized using the neutron time-of-flight (nTOF) line on Geneseo's 1.7 MV tandem Pelletron accelerator. Neutron signals can be differentiated from gamma signals by employing coincidence methods. A 1.8-MeV beam of deuterons incident on a deuterated polyethylene target produces neutrons via the 2H(d,n)3He reaction. Neutrons emerging at a lab angle of 88° have an energy of 2.96 MeV; the 3He ions associated with these neutrons are detected at a scattering angle of 43° using a surface barrier detector. The time of flight of the neutron can be measured by using the 3He detection as a ``start'' signal and the scintillation detection as a ``stop'' signal. This time of flight requirement is used to identify the 2.96-MeV neutron signals in the scintillator. To measure the light curve produced by these monoenergetic neutrons, two photomultiplier (PMT) tubes are attached to the scintillator. The full aperture PMT establishes the nTOF coincidence. The other PMT is fitted with a pinhole to collect single events. The time between the full aperture PMT signal and the arrival of the signal in the pinhole PMT is used to determine the light curve for the scintillator. This system will enable the neutron response of various scintillators to be compared. Supported in part by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Rapid Identification and Assignation of the Active Ingredients in Fufang Banbianlian Injection Using HPLC-DAD-ESI-IT-TOF-MS.

PubMed

Li, Sensen; Lin, Zongtao; Jiang, Haixiu; Tong, Lingkun; Wang, Hong; Chen, Shizhong

2016-08-01

Fufang Banbianlian Injection (FBI) is a well-known traditional Chinese medicine formula composed of three herbal medicines. However, the systematic investigation on its chemical components has not been reported yet. In this study, a high-performance liquid chromatography combined with diode-array detector, and coupled to an electrospray ionization with ion-trap time-of-flight mass spectrometry (HPLC-DAD-ESI-IT-TOF-MS) method, was established for the identification of chemical profile in FBI. Sixty-six major constituents (14 phenolic acids, 14 iridoids, 20 flavonoids, 2 benzylideneacetone compounds, 3 phenylethanoid glycosides, 1 coumarin, 1 lignan, 3 nucleosides, 1 amino acids, 1 monosaccharides, 2 oligosaccharides, 3 alduronic acids and citric acid) were identified or tentatively characterized by comparing their retention times and MS spectra with those of standards or literature data. Finally, all constituents were further assigned in the individual herbs (InHs), although some of them were from multiple InHs. As a result, 11 compounds were from Lobelia chinensis Lour, 33 compounds were from Scutellaria barbata D. Don and 38 compounds were from Hedyotis diffusa Willd. In conclusion, the developed HPLC-DAD-ESI-IT-TOF-MS method is a rapid and efficient technique for analysis of FBI sample, and could be a valuable method for the further study on the quality control of the FBI. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Measuring time of flight of fusion products in an inertial electrostatic confinement fusion device for spatial profiling of fusion reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donovan, D. C.; Boris, D. R.; Kulcinski, G. L.

2013-03-15

A new diagnostic has been developed that uses the time of flight (TOF) of the products from a nuclear fusion reaction to determine the location where the fusion reaction occurred. The TOF diagnostic uses charged particle detectors on opposing sides of the inertial electrostatic confinement (IEC) device that are coupled to high resolution timing electronics to measure the spatial profile of fusion reactions occurring between the two charged particle detectors. This diagnostic was constructed and tested by the University of Wisconsin-Madison Inertial Electrostatic Confinement Fusion Group in the IEC device, HOMER, which accelerates deuterium ions to fusion relevant energies inmore » a high voltage ({approx}100 kV), spherically symmetric, electrostatic potential well [J. F. Santarius, G. L. Kulcinski, R. P. Ashley, D. R. Boris, B. B. Cipiti, S. K. Murali, G. R. Piefer, R. F. Radel, T. E. Radel, and A. L. Wehmeyer, Fusion Sci. Technol. 47, 1238 (2005)]. The TOF diagnostic detects the products of D(d,p)T reactions and determines where along a chord through the device the fusion event occurred. The diagnostic is also capable of using charged particle spectroscopy to determine the Doppler shift imparted to the fusion products by the center of mass energy of the fusion reactants. The TOF diagnostic is thus able to collect spatial profiles of the fusion reaction density along a chord through the device, coupled with the center of mass energy of the reactions occurring at each location. This provides levels of diagnostic detail never before achieved on an IEC device.« less

Interfacial micropore defect formation in PEDOT:PSS-Si hybrid solar cells probed by TOF-SIMS 3D chemical imaging.

PubMed

Thomas, Joseph P; Zhao, Liyan; Abd-Ellah, Marwa; Heinig, Nina F; Leung, K T

2013-07-16

Conducting p-type polymer layers on n-type Si have been widely studied for the fabrication of cost-effective hybrid solar cells. In this work, time-of-flight secondary ion mass spectrometry (TOF-SIMS) is used to provide three-dimensional chemical imaging of the interface between poly(3,4-ethylene-dioxythiophene):polystyrenesulfonate (PEDOT:PSS) and SiOx/Si in a hybrid solar cell. To minimize structural damage to the polymer layer, an Ar cluster sputtering source is used for depth profiling. The present result shows the formation of micropore defects in the interface region of the PEDOT:PSS layer on the SiOx/Si substrate. This interfacial micropore defect formation becomes more prominent with increasing thickness of the native oxide layer, which is a key device parameter that greatly affects the hybrid solar cell performance. Three-dimensional chemical imaging coupled with Ar cluster ion sputtering has therefore been demonstrated as an emerging technique for probing the interface of this and other polymer-inorganic systems.

Comprehensive characterization of the in vitro and in vivo metabolites of limonin in human samples using LC-Q-TOF/MS.

PubMed

Liu, Shijia; Chen, Peidong; Zhang, Nongshan; Sun, Luning; Dai, Guoliang; Zhu, Lei; Li, Changyin; Zhao, Yang; Zhang, Li; Fu, Haiyan; Ju, Wenzheng

2017-11-15

Limonin is a bitter triterpenoid dilactone in the genus Citrus with potential medicinal value. In this study, the metabolism of limonin in human was characterized by high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS). A total of 7 metabolites were identified from human samples. Among them, 3 metabolites of M1, M2 and M4 were detected in urine and feces, and the others were found in intestinal bacteria sample. Notably, M1 and M3 were chemically synthesized, of which the structures were further confirmed by NMR spectra data. The metabolism of limonin involved three major pathways, namely, reduction, hydrolysis and methylation. The reduction and hydrolysis were commonly observed in ring D of limonin. The metabolites showed decomposition in ring A. This study provides data for the metabolism of limonin in humans, and will contribute to explain its biological activity. Copyright © 2017. Published by Elsevier B.V.

Metabolites profiling of Pulsatilla saponin D in rat by ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS/MS).

PubMed

Ouyang, Hui; Zhou, Maofu; Guo, Yicheng; He, Mingzhen; Huang, Hesong; Ye, Xide; Feng, Yulin; Zhou, Xin; Yang, Shilin

2014-07-01

Pulsatilla saponin D, an antitumor substance isolated from traditional Chinese herbal medicine Pulsatilla chinensis (Bge.) Regel, is a promising candidate for new drug development. The purpose of the present study is to establish a simple and practical strategy for the metabolite profiling of Pulsatilla saponin D in vivo. A total of 18 metabolites were identified in rat plasma, urine and feces samples based on MS and MS/MS data by using ESI-Q-TOF-MS/MS, and eight of them (M11-M18) were reported for the first time. The results indicated that deglycosylation, dehydrogenation, hydroxylation and sulfation were the major metabolic transformations of Pulsatilla saponin D in vivo. This study has improved our understanding of the metabolic fate of Pulsatilla saponin D in vivo, and the information gained from the current study is relevant to the pharmacological activity of Pulsatilla saponin D. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomic Analysis of Albumins and Globulins from Wheat Variety Chinese Spring and Its Fine Deletion Line 3BS-8

PubMed Central

Ma, Chao-Ying; Gao, Li-Yan; Li, Ning; Li, Xiao-Hui; Ma, Wu-Jun; Appels, Rudi; Yan, Yue-Ming

2012-01-01

The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance variation (p < 0.05) in matured wheat grains and 21 spots were identified by tandem MALDI-TOF/TOF-MS. Among the identified spots, four were cultivar-specific, including three (spots B15, B16, and B21) in Chinese Spring and one in 3BS-8 (spot B10). Among variety-different DEPs between Chinese Spring and 3BS-8, most spots showed a higher express profile in CS; only four spots showed up-regulated expression tendency in 3BS-8. An interesting observation was that more than half of the identified protein spots were involved in storage proteins, of which 11 spots were identified as globulins. According to these results, we can presume that the encoded genes of protein spots B15, B16, and B21 were located on the chromosome segment deleted in 3BS-8. PMID:23202959

Direct Assessment of Wall Shear Stress by Signal Intensity Gradient from Time-of-Flight Magnetic Resonance Angiography

PubMed Central

Lee, Sang Hyuk; Ryu, Han Uk; Park, Se-Hyoung; Chung, Gyung-Ho; Cho, Young I.

2017-01-01

The aim of the study was to calculate the arterial wall signal intensity gradient (SIG) from time-of-flight MR angiography (TOF-MRA) and represent arterial wall shear stress. We developed a new algorithm that uses signal intensity (SI) of a TOF-MRA to directly calculate the signal intensity gradient (SIG). The results from our phantom study showed that the TOF-MRA SIG could be used to distinguish the magnitude of blood flow rate as high (mean SIG ± SD, 2.2 ± 0.4 SI/mm for 12.5 ± 2.3 L/min) and low (0.9 ± 0.3 SI/mm for 8.5 ± 2.6 L/min) in vessels (p < 0.001). Additionally, we found that the TOF-MRA SIG values were highly correlated with various flow rates (β = 0.96, p < 0.001). Remarkably, the correlation coefficient between the WSS obtained from the computational fluid dynamics (CFD) analysis and the TOF-MRA SIG was greater than 0.8 in each section at the carotid artery (p < 0.001 for all β values). This new technique using TOF-MRA could enable the rapid calculation of the TOF-MRA SIG and thereby the WSS. Thus, the TOF-MRA SIG can provide clinicians with an accurate and efficient screening method for making rapid decisions on the risk of vascular disease for a patient in clinical practice. PMID:28900625

Direct Assessment of Wall Shear Stress by Signal Intensity Gradient from Time-of-Flight Magnetic Resonance Angiography.

PubMed

Han, Kap-Soo; Lee, Sang Hyuk; Ryu, Han Uk; Park, Se-Hyoung; Chung, Gyung-Ho; Cho, Young I; Jeong, Seul-Ki

2017-01-01

The aim of the study was to calculate the arterial wall signal intensity gradient (SIG) from time-of-flight MR angiography (TOF-MRA) and represent arterial wall shear stress. We developed a new algorithm that uses signal intensity (SI) of a TOF-MRA to directly calculate the signal intensity gradient (SIG). The results from our phantom study showed that the TOF-MRA SIG could be used to distinguish the magnitude of blood flow rate as high (mean SIG ± SD, 2.2 ± 0.4 SI/mm for 12.5 ± 2.3 L/min) and low (0.9 ± 0.3 SI/mm for 8.5 ± 2.6 L/min) in vessels ( p < 0.001). Additionally, we found that the TOF-MRA SIG values were highly correlated with various flow rates ( β = 0.96, p < 0.001). Remarkably, the correlation coefficient between the WSS obtained from the computational fluid dynamics (CFD) analysis and the TOF-MRA SIG was greater than 0.8 in each section at the carotid artery ( p < 0.001 for all β values). This new technique using TOF-MRA could enable the rapid calculation of the TOF-MRA SIG and thereby the WSS. Thus, the TOF-MRA SIG can provide clinicians with an accurate and efficient screening method for making rapid decisions on the risk of vascular disease for a patient in clinical practice.

First case of breakthrough pneumonia due to Aspergillus nomius in a patient with acute myeloid leukemia.

PubMed

Caira, Morena; Posteraro, Brunella; Sanguinetti, Maurizio; de Carolis, Elena; Leone, Giuseppe; Pagano, Livio

2012-10-01

We report the first known case of a breakthrough pulmonary infection caused by Aspergillus nomius in an acute myeloid leukemia patient receiving caspofungin therapy. The isolate was identified using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and sequencing-based methods. The organism was found to be fully susceptible, in vitro, to echinocandin antifungal agents.

Follow-up assessment of coiled intracranial aneurysms using zTE MRA as compared with TOF MRA: a preliminary image quality study.

PubMed

Shang, Song'an; Ye, Jing; Luo, Xianfu; Qu, Jianxun; Zhen, Yong; Wu, Jingtao

2017-10-01

To prospectively assess coiled intracranial aneurysms using a novel non-contrast enhanced zero echo time (zTE) MR angiography (MRA) method, and compare its image quality with time-of-flight (TOF) MRA, using digital subtraction angiography (DSA) as reference. Twenty-five patients (10 males and 15 females; age 53.96 ± 12.46 years) were enrolled in this monocentric study. MRA sequences were performed 24 h before DSA. Susceptibility artefact intensity and flow signal within the parent artery were carried out using a 4-point scale. Occlusion status was assessed using the 3-grade Montreal scale. Scores of zTE were higher than TOF for both susceptibility artefact intensity (3.42 ± 0.64, 2.92 ± 0.63, P = 0.01) and flow signal (3.66 ± 0.95, 3.24 ± 1.24, P = 0.01). DSA revealed 17 complete occlusions, five residual neck aneurysms and two residual aneurysms. Inter-observer agreement was excellent (weighted κ: 0.89) for zTE and good (weighted κ: 0.68) for TOF. Intermodality agreement was excellent for zTE (weighted κ: 0.95) and good for TOF (weighted κ: 0.80). Correlations of both MRA sequences with DSA were high (zTE, Spearman's ρ: 0.91; TOF, Spearman's ρ: 0.81). zTE MRA showed promising results for follow-up assessment of coiled intracranial aneurysms and was superior to TOF MRA for visualizing the parent artery and evaluating occlusion status. • Various MRA sequences were applied for follow-up assessment of coiled intracranial aneurysms. • zTE MRA was less sensitive to susceptibility artefacts and haemodynamics. • In this monocentric study, zTE MRA was equivalent to DSA. • zTE MRA maybe an alternative to TOF MRA for follow-up assessment.

Screening and Identification for Immunological Active Components from Andrographis Herba Using Macrophage Biospecific Extraction Coupled with UPLC/Q-TOF-MS.

PubMed

Wang, Yaqi; Jiao, Jiaojiao; Yang, Yuanzhen; Yang, Ming; Zheng, Qin

2018-04-30

The method of cell biospecific extraction coupled with UPLC/Q-TOF-MS has been developed as a tool for the screening and identification of potential immunological active components from Andrographis Herba (AH). In our study, a macrophage cell line (RAW264.7) was used to extract cell-combining compounds from the ethanol extract of AH. The cell binding system was then analyzed and identified by UPLC/Q-TOF-MS analysis. Finally, nine compounds, which could combine with macrophages, in an ethanol extract of AH were detected by comparing basic peak intensity (BPI) profiles of macrophages before and after treatment with AH. Then they were identified as Andrographidine E ( 1 ), Andrographidine D ( 2 ), Neoandrographolide ( 3 ), Dehydroandrographolide ( 4 ), 5, 7, 2′, 3′-tetramethoxyflavone ( 5 ), β-sitosterol ( 7 ), 5-hydroxy-7, 2′, 3′-trimethoxyflavone ( 8 ) and 5-hydroxy-7, 8, 2′, 3′-tetramethoxyflavone ( 9 ), which could classified into five flavonoids, three diterpene lactones, and one sterol. Their structures were recognized by their characteristic fragment ions and fragmentations pattern of diterpene lactones and flavonoids. Additionally, the activity of compounds 3 , 4 , and 7 was tested in vitro. Results showed that these three compounds could decrease the release of NO ( p < 0.01) in macrophages remarkably. Moreover, 3 , 4 , and 7 showed satisfactory dose-effect relationships and their IC 50 values were 9.03, 18.18, and 13.76 μg/mL, respectively. This study is the first reported work on the screening of immunological active components from AH. The potential immunological activity of flavonoids from AH has not been reported previously.

A magnetic particle time-of-flight (MagPTOF) diagnostic for measurements of shock- and compression-bang time at the NIF (invited).

PubMed

Rinderknecht, H G; Sio, H; Frenje, J A; Magoon, J; Agliata, A; Shoup, M; Ayers, S; Bailey, C G; Gatu Johnson, M; Zylstra, A B; Sinenian, N; Rosenberg, M J; Li, C K; Sèguin, F H; Petrasso, R D; Rygg, J R; Kimbrough, J R; Mackinnon, A; Bell, P; Bionta, R; Clancy, T; Zacharias, R; House, A; Döppner, T; Park, H S; LePape, S; Landen, O; Meezan, N; Robey, H; Glebov, V U; Hohenberger, M; Stoeckl, C; Sangster, T C; Li, C; Parat, J; Olson, R; Kline, J; Kilkenny, J

2014-11-01

A magnetic particle time-of-flight (MagPTOF) diagnostic has been designed to measure shock- and compression-bang time using D(3)He-fusion protons and DD-fusion neutrons, respectively, at the National Ignition Facility (NIF). This capability, in combination with shock-burn weighted areal density measurements, will significantly constrain the modeling of the implosion dynamics. This design is an upgrade to the existing particle time-of-flight (pTOF) diagnostic, which records bang times using DD or DT neutrons with an accuracy better than ±70 ps [H. G. Rinderknecht et al., Rev. Sci. Instrum. 83, 10D902 (2012)]. The inclusion of a deflecting magnet will increase D(3)He-proton signal-to-background by a factor of 1000, allowing for the first time simultaneous measurements of shock- and compression-bang times in D(3)He-filled surrogate implosions at the NIF.

The VOICES/VOCES success story: effective strategies for training, technical assistance and community-based organization implementation.

PubMed

Hamdallah, Myriam; Vargo, Sue; Herrera, Jennifer

2006-08-01

The Centers for Disease Control and Prevention's Diffusion of Effective Behavioral Interventions (DEBI) project successfully disseminated VOICES/VOCES, a brief video-based HIV risk reduction intervention targeting African American and Latino heterosexual men and women at risk for HIV infection. Elements of the dissemination strategy included a comprehensive and user-friendly intervention kit, comprising (a) an implementationmanual and othermaterials necessary for conducting the intervention (b) a Training of Facilitators (TOF) curriculum used to teach agency staff how to implement the EBI in their setting, (c) a network of expert trainers who attend a training institute to become adept at using the TOF curriculum to train facilitators, (d) a comprehensive training coordination center to plan and deliver TOF trainings, (e) proactive technical assistance to trainers, and (f) post-TOF technical assistance for local implementers. This article reports on those strategies and a local CBO's successful participation in DEBI, resulting implementation of VOICES/VOCES, with unique approaches to adaptation and tailoring.

A Small Molecule that Mimics the BB-Loop in the Toll/IL-1 Receptor Domain of MyD88 Attenuates Staphylococcal Enterotoxin B Induced Pro-Inflammatory Cytokine Production and Toxicity in Mice

DTIC Science & Technology

2011-06-01

121.8, 114.6, 67.0, 55.1, 46.6, 45.7, 31.3, 25.9, 24.0, 19.4, 17.6; HRMS: (ESI-TOF) C17H24N2O3H+ expected: 305.1860. found: 305.1860. (S)-1- benzyl -3...chemiluminescent substrate in the presence of hydrogen peroxide using Immun-Star WesternC Chemiluminescent Kit (BioRad). An imaging system VersaDoc Model

Development of a new protocol for rapid bacterial identification and susceptibility testing directly from urine samples.

PubMed

Zboromyrska, Y; Rubio, E; Alejo, I; Vergara, A; Mons, A; Campo, I; Bosch, J; Marco, F; Vila, J

2016-06-01

The current gold standard method for the diagnosis of urinary tract infections (UTI) is urine culture that requires 18-48 h for the identification of the causative microorganisms and an additional 24 h until the results of antimicrobial susceptibility testing (AST) are available. The aim of this study was to shorten the time of urine sample processing by a combination of flow cytometry for screening and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for bacterial identification followed by AST directly from urine. The study was divided into two parts. During the first part, 675 urine samples were processed by a flow cytometry device and a cut-off value of bacterial count was determined to select samples for direct identification by MALDI-TOF-MS at ≥5 × 10(6) bacteria/mL. During the second part, 163 of 1029 processed samples reached the cut-off value. The sample preparation protocol for direct identification included two centrifugation and two washing steps. Direct AST was performed by the disc diffusion method if a reliable direct identification was obtained. Direct MALDI-TOF-MS identification was performed in 140 urine samples; 125 of the samples were positive by urine culture, 12 were contaminated and 3 were negative. Reliable direct identification was obtained in 108 (86.4%) of the 125 positive samples. AST was performed in 102 identified samples, and the results were fully concordant with the routine method among 83 monomicrobial infections. In conclusion, the turnaround time of the protocol described to diagnose UTI was about 1 h for microbial identification and 18-24 h for AST. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Lyman α photolysis of solid nitromethane (CH3NO2) and D3-nitromethane (CD3NO2)--untangling the reaction mechanisms involved in the decomposition of model energetic materials.

PubMed

Maksyutenko, Pavlo; Muzangwa, Lloyd G; Jones, Brant M; Kaiser, Ralf I

2015-03-21

Solid nitromethane (CH3NO2) along with its isotopically labelled counterpart D3-nitromethane (CD3NO2) ices were exposed to Lyman α photons to investigate the mechanism involved in the decomposition of energetic materials in the condensed phase. The chemical processes in the ices were monitored online and in situ via infrared spectroscopy complimented by temperature programmed desorption studies utilizing highly sensitive reflectron time-of-flight mass spectrometry coupled with pulsed photoionization (ReTOF-PI) at 10.49 eV. The infrared data revealed the formation of cis-methylnitrite (CH3ONO), formaldehyde (H2CO), water (H2O), carbon monoxide (CO), and carbon dioxide (CO2). Upon sublimation of the irradiated samples, three classes of higher molecular weight products, which are uniquely formed in the condensed phase, were identified via ReTOF-PI: (i) nitroso compounds [nitrosomethane (CH3NO), nitrosoethane (C2H5NO), nitrosopropane (C3H7NO)], (ii) nitrite compounds [methylnitrite (CH3ONO), ethylnitrite (C2H5ONO), propylnitrite (C3H7ONO)], and (iii) higher molecular weight molecules [CH3NONOCH3, CH3NONO2CH3, CH3OCH2NO2, ONCH2CH2NO2]. The mechanistical information obtained in the present study suggest that the decomposition of nitromethane in the condensed phase is more complex compared to the gas phase under collision-free conditions opening up not only hitherto unobserved decomposition pathways of nitromethane (hydrogen atom loss, oxygen atom loss, retro carbene insertion), but also the blocking of several initial decomposition steps due to the 'matrix cage effect'.

157 nm Photodissociation of Dipeptide Ions Containing N-Terminal Arginine

NASA Astrophysics Data System (ADS)

Webber, Nathaniel; He, Yi; Reilly, James P.

2014-02-01

Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m2 and m2+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.

Characterizing ICF Neutron Diagnostics on the nTOF line at SUNY Geneseo

NASA Astrophysics Data System (ADS)

Simone, Angela; Padalino, Stephen; Turner, Ethan; Ginnane, Mary Kate; Dubois, Natalie; Fletcher, Kurtis; Giordano, Michael; Lawson-Keister, Patrick; Harrison, Hannah; Visca, Hannah; Sangster, Craig; Regan, Sean

2014-10-01

Charged particle beams from the Geneseo 1.7 MV tandem Pelletron accelerator produce nuclear reactions that emit neutrons in the range of 0.5 to 17.9 MeV via the d(d,n)3He and 11B(d,n)12C reactions. The neutron energy and flux can be adjusted by controlling the accelerator beam current and potential. This adjustable neutron source makes it possible to calibrate ICF and HEDP neutron scintillator diagnostics. However, gamma rays which are often present during an accelerator-based calibration are difficult to differentiate from neutron signals in scintillators. To identify neutrons from gamma rays and to determine their energy, a permanent neutron time-of-flight (nTOF) line is being constructed. By detecting the scintillator signal in coincidence with an associated charged particle (ACP) produced in the reaction, the identity of the neutron can be known and its energy determined by time of flight. Using a 100% efficient surface barrier detector to count the ACPs, the absolute efficiency of the scintillator as a function of neutron energy can be determined. This is done by determining the ratio of the ACP counts in the singles spectrum to coincidence counts for matched solid angles of the SBD and scintillator. Funded in part by a LLE contract through the DOE.

GATE Monte Carlo simulations for variations of an integrated PET/MR hybrid imaging system based on the Biograph mMR model

NASA Astrophysics Data System (ADS)

Aklan, B.; Jakoby, B. W.; Watson, C. C.; Braun, H.; Ritt, P.; Quick, H. H.

2015-06-01

A simulation toolkit, GATE (Geant4 Application for Tomographic Emission), was used to develop an accurate Monte Carlo (MC) simulation of a fully integrated 3T PET/MR hybrid imaging system (Siemens Biograph mMR). The PET/MR components of the Biograph mMR were simulated in order to allow a detailed study of variations of the system design on the PET performance, which are not easy to access and measure on a real PET/MR system. The 3T static magnetic field of the MR system was taken into account in all Monte Carlo simulations. The validation of the MC model was carried out against actual measurements performed on the PET/MR system by following the NEMA (National Electrical Manufacturers Association) NU 2-2007 standard. The comparison of simulated and experimental performance measurements included spatial resolution, sensitivity, scatter fraction, and count rate capability. The validated system model was then used for two different applications. The first application focused on investigating the effect of an extension of the PET field-of-view on the PET performance of the PET/MR system. The second application deals with simulating a modified system timing resolution and coincidence time window of the PET detector electronics in order to simulate time-of-flight (TOF) PET detection. A dedicated phantom was modeled to investigate the impact of TOF on overall PET image quality. Simulation results showed that the overall divergence between simulated and measured data was found to be less than 10%. Varying the detector geometry showed that the system sensitivity and noise equivalent count rate of the PET/MR system increased progressively with an increasing number of axial detector block rings, as to be expected. TOF-based PET reconstructions of the modeled phantom showed an improvement in signal-to-noise ratio and image contrast to the conventional non-TOF PET reconstructions. In conclusion, the validated MC simulation model of an integrated PET/MR system with an overall accuracy error of less than 10% can now be used for further MC simulation applications such as development of hardware components as well as for testing of new PET/MR software algorithms, such as assessment of point-spread function-based reconstruction algorithms.

A 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce detector with dual-sided digital photon counter readout for ultrahigh-performance TOF-PET and TOF-PET/MRI

NASA Astrophysics Data System (ADS)

Borghi, Giacomo; Peet, Bart Jan; Tabacchini, Valerio; Schaart, Dennis R.

2016-07-01

New applications for positron emission tomography (PET) and combined PET/magnetic resonance imaging (MRI) are currently emerging, for example in the fields of neurological, breast, and pediatric imaging. Such applications require improved image quality, reduced dose, shorter scanning times, and more precise quantification. This can be achieved by means of dedicated scanners based on ultrahigh-performance detectors, which should provide excellent spatial resolution, precise depth-of-interaction (DOI) estimation, outstanding time-of-flight (TOF) capability, and high detection efficiency. Here, we introduce such an ultrahigh-performance TOF/DOI PET detector, based on a 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce crystal. The 32 mm  ×  32 mm front and back faces of the crystal are coupled to a digital photon counter (DPC) array, in so-called dual-sided readout (DSR) configuration. The fully digital detector offers a spatial resolution of ~1.1 mm full width at half maximum (FWHM)/~1.2 mm mean absolute error, together with a DOI resolution of ~2.4 mm FWHM, an energy resolution of 10.2% FWHM, and a coincidence resolving time of 147 ps FWHM. The time resolution closely approaches the best results (135 ps FWHM) obtained to date with small crystals made from the same material coupled to the same DPC arrays, illustrating the excellent correction for optical and electronic transit time spreads that can be achieved in monolithic scintillators using maximum-likelihood techniques for estimating the time of interaction. The performance barely degrades for events with missing data (up to 6 out of 32 DPC dies missing), permitting the use of almost all events registered under realistic acquisition conditions. Moreover, the calibration procedures and computational methods used for position and time estimation follow recently made improvements that make them fast and practical, opening up realistic perspectives for using DSR monolithic scintillator detectors in TOF-PET and TOF-PET/MRI systems.

Hemodynamic vascular biomarkers for initiation of paraclinoid internal carotid artery aneurysms using patient-specific computational fluid dynamic simulation based on magnetic resonance imaging.

PubMed

Watanabe, Tomoya; Isoda, Haruo; Takehara, Yasuo; Terada, Masaki; Naito, Takehiro; Kosugi, Takafumi; Onishi, Yuki; Tanoi, Chiharu; Izumi, Takashi

2018-05-01

We performed computational fluid dynamics (CFD) for patients with and without paraclinoid internal carotid artery (ICA) aneurysms to evaluate the distribution of vascular biomarkers at the aneurysm initiation sites of the paraclinoid ICA. This study included 35 patients who were followed up for aneurysms using 3D time of flight (TOF) magnetic resonance angiography (MRA) and 3D cine phase-contrast MR imaging. Fifteen affected ICAs were included in group A with the 15 unaffected contralateral ICAs in group B. Thirty-three out of 40 paraclinoid ICAs free of aneurysms and arteriosclerotic lesions were included in group C. We deleted the aneurysms in group A based on the 3D TOF MRA dataset. We performed CFD based on MR data set and obtained wall shear stress (WSS), its derivatives, and streamlines. We qualitatively evaluated their distributions at and near the intracranial aneurysm initiation site among three groups. We also calculated and compared the normalized highest (nh-) WSS and nh-spatial WSS gradient (SWSSG) around the paraclinoid ICA among three groups. High WSS and SWSSG distribution were observed at and near the aneurysm initiation site in group A. High WSS and SWSSG were also observed at similar locations in group B and group C. However, nh-WSS and nh-SWSSG were significantly higher in group A than in group C, and nh-SWSSG was significantly higher in group A than in group B. Our findings indicated that nh-WSS and nh-SWSSG were good biomarkers for aneurysm initiation in the paraclinoid ICA.

Vessel segmentation in 4D arterial spin labeling magnetic resonance angiography images of the brain

NASA Astrophysics Data System (ADS)

Phellan, Renzo; Lindner, Thomas; Falcão, Alexandre X.; Forkert, Nils D.

2017-03-01

4D arterial spin labeling magnetic resonance angiography (4D ASL MRA) is a non-invasive and safe modality for cerebrovascular imaging procedures. It uses the patient's magnetically labeled blood as intrinsic contrast agent, so that no external contrast media is required. It provides important 3D structure and blood flow information but a sufficient cerebrovascular segmentation is important since it can help clinicians to analyze and diagnose vascular diseases faster, and with higher confidence as compared to simple visual rating of raw ASL MRA images. This work presents a new method for automatic cerebrovascular segmentation in 4D ASL MRA images of the brain. In this process images are denoised, corresponding image label/control image pairs of the 4D ASL MRA sequences are subtracted, and temporal intensity averaging is used to generate a static representation of the vascular system. After that, sets of vessel and background seeds are extracted and provided as input for the image foresting transform algorithm to segment the vascular system. Four 4D ASL MRA datasets of the brain arteries of healthy subjects and corresponding time-of-flight (TOF) MRA images were available for this preliminary study. For evaluation of the segmentation results of the proposed method, the cerebrovascular system was automatically segmented in the high-resolution TOF MRA images using a validated algorithm and the segmentation results were registered to the 4D ASL datasets. Corresponding segmentation pairs were compared using the Dice similarity coefficient (DSC). On average, a DSC of 0.9025 was achieved, indicating that vessels can be extracted successfully from 4D ASL MRA datasets by the proposed segmentation method.

Procedure Enabling Simulation and In-Depth Analysis of Optical Effects in Camera-Based Time-Of Sensors

NASA Astrophysics Data System (ADS)

Baumgart, M.; Druml, N.; Consani, M.

2018-05-01

This paper presents a simulation approach for Time-of-Flight cameras to estimate sensor performance and accuracy, as well as to help understanding experimentally discovered effects. The main scope is the detailed simulation of the optical signals. We use a raytracing-based approach and use the optical path length as the master parameter for depth calculations. The procedure is described in detail with references to our implementation in Zemax OpticStudio and Python. Our simulation approach supports multiple and extended light sources and allows accounting for all effects within the geometrical optics model. Especially multi-object reflection/scattering ray-paths, translucent objects, and aberration effects (e.g. distortion caused by the ToF lens) are supported. The optical path length approach also enables the implementation of different ToF senor types and transient imaging evaluations. The main features are demonstrated on a simple 3D test scene.

Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry.

PubMed

Haiko, Johanna; Savolainen, Laura E; Hilla, Risto; Pätäri-Sampo, Anu

2016-10-01

Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3h at 35°C with 5% CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5)cfu/ml in culture (n=107), compared with conventional culture method. However, Gram-positive bacteria (n=28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24h to 4-6h. Copyright © 2016 Elsevier B.V. All rights reserved.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry.

PubMed

Maslen, Sarah; Sadowski, Pawel; Adam, Alex; Lilley, Kathryn; Stephens, Elaine

2006-12-15

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Determination of the structure of subsurface layers by means of coaxial time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Wang, Y.; Teplov, S. V.; Rabalais, J. W.

1994-05-01

It is demonstrated that both surface and subsurface structural information can be obtained from Si{100}-(2 × 1) and Si{100}-(1 × 1)-H by coupling coaxial time-of-flight scattering and recoiling spectrometry (TOF-SARS) with three-dimensional trajectory simulations. Experimentally, backscattering intensity versus incident α angle scans at a scattering angle of ˜ 180° have been measured for 2 keV He + incident on both the (2 × 1) and (1 × 1)-H surfaces. Computationally, an efficient three-dimensional version of the Monte Carlo computer code RECAD has been developed and applied to simulation of the TOF-SARS results. An R (reliability) factor has been introduced for quantitative evaluation of the agreement between experimental and simulated scans. For the case of 2 keV He + scattering from Si{100}, scattering features can be observed and delineated from as many as 14 atomic layers ( ˜ 18 Å) below the surface. The intradimer spacing D is determined as 2.2 Å from the minimum in the R-factor versus D plot.

High-energy Collision-induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

PubMed Central

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

2014-01-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote-fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers. PMID:24781458

High-energy collision-induced dissociation by MALDI TOF/TOF causes charge-remote fragmentation of steroid sulfates.

PubMed

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B; Holy, Timothy E; Gross, Michael L

2014-08-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

On the local well-posedness and a Prodi-Serrin-type regularity criterion of the three-dimensional MHD-Boussinesq system without thermal diffusion

NASA Astrophysics Data System (ADS)

Larios, Adam; Pei, Yuan

2017-07-01

We prove a Prodi-Serrin-type global regularity condition for the three-dimensional Magnetohydrodynamic-Boussinesq system (3D MHD-Boussinesq) without thermal diffusion, in terms of only two velocity and two magnetic components. To the best of our knowledge, this is the first Prodi-Serrin-type criterion for such a 3D hydrodynamic system which is not fully dissipative, and indicates that such an approach may be successful on other systems. In addition, we provide a constructive proof of the local well-posedness of solutions to the fully dissipative 3D MHD-Boussinesq system, and also the fully inviscid, irresistive, non-diffusive MHD-Boussinesq equations. We note that, as a special case, these results include the 3D non-diffusive Boussinesq system and the 3D MHD equations. Moreover, they can be extended without difficulty to include the case of a Coriolis rotational term.

Dynamics of the C/H and C/F exchanges in the reaction of 3P carbon atoms with vinyl fluoride

NASA Astrophysics Data System (ADS)

Lee, Shih-Huang; Chen, Wei-Kan; Chin, Chih-Hao; Huang, Wen-Jian

2013-08-01

Two product channels C3H2F + H and C3H3 + F were identified in the reaction of C(3P) atoms with vinyl fluoride (C2H3F) at collision energy 3.7 kcal mol-1 in a crossed molecular-beam apparatus using selective photoionization. Time-of-flight (TOF) spectra of products C3H2F and C3H3 were measured at 12-16 laboratory angles as well as a TOF spectrum of atomic F, a counter part of C3H3, was recorded at single laboratory angle. From the best simulation of product TOF spectra, translational-energy distributions at seven scattering angles and a nearly isotropic (forward and backward peaked) angular distribution were derivable for exit channel C3H2F + H (C3H3 + F) that has average kinetic-energy release of 14.5 (4.9) kcal mol-1. Products C3H2F + H and C3H3 + F were estimated to have a branching ratio of ˜53:47. Furthermore, TOF spectra and photoionization spectra of products C3H2F and C3H3 were measured at laboratory angle 62° with photoionization energy ranging from 7 eV to 11.6 eV. The appearance of TOF spectra is insensitive to photon energy, implying that only single species overwhelmingly contributes to products C3H2F and C3H3. HCCCHF (H2CCCH) was identified as the dominant species based on the measured ionization threshold of 8.3 ± 0.2 (8.6 ± 0.2) eV and the maximal translational-energy release. The C/H and C/F exchange mechanisms are stated.

Shiga Toxin 2 Subtypes of Enterohemorrhagic E. coli O157:H- E32511 Analyzed by RT-qPCR and Top-Down Proteomics Using MALDI-TOF-TOF-MS

NASA Astrophysics Data System (ADS)

Fagerquist, Clifton K.; Zaragoza, William J.

2015-05-01

We have measured the relative abundance of the B-subunits and mRNA transcripts of two Stx2 subtypes present in Shiga toxin-producing Escherichia coli (STEC) O157:H- strain E32511 using matrix-assisted laser desorption/ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-MS/MS) with post source decay (PSD) and real time-quantitative polymerase chain reaction (RT-qPCR). Stx2a and Stx2c in STEC strain E32511 were quantified from the integrated peak area of their singly charged disulfide-intact B-subunit ions at m/z ~7819 and m/z ~7774, respectively. We found that the Stx2a subtype was 21-fold more abundant than the Stx2c subtype. The two amino acid substitutions (16D ↔ 16 N and 24D ↔ 24A) that distinguish Stx2a from Stx2c not only result in a mass difference of 45 Da between their respective B-subunits but also result in distinctly different fragmentation channels by MS/MS-PSD because both substitutions involve an aspartic acid (D) residue. Importantly, these two substitutions have also been linked to differences in subtype toxicity. We measured the relative abundances of mRNA transcripts using RT-qPCR and determined that the stx2a transcript is 13-fold more abundant than stx2c transcript. In silico secondary structure analysis of the full mRNA operons of stx2a and stx2c suggest that transcript structural differences may also contribute to a relative increase of Stx2a over Stx2c. In consequence, toxin expression may be under both transcriptional and post-transcriptional control.

Tea catechins and flavonoids from the leaves of Camellia sinensis inhibit yeast alcohol dehydrogenase.

PubMed

Manir, Md Maniruzzaman; Kim, Jeong Kee; Lee, Byeong-Gon; Moon, Surk-Sik

2012-04-01

Four new quercetin acylglycosides, designated camelliquercetisides A-D, quercetin 3-O-[α-L-arabinopyranosyl(1→3)][2-O″-(E)-p-coumaroyl][β-D-glucopyranosyl(1→3)-α-L-rhamnopyranosyl(1→6)]-β-D-glucoside (17), quercetin 3-O-[2-O″-(E)-p-coumaroyl][β-D-glucopyranosyl(1→3)-α-L-rhamnopyranosyl(1→6)]-β-D-glucoside (18), quercetin 3-O-[α-L-arabinopyranosyl(1→3)][2-O″-(E)-p-coumaroyl][α-L-rhamnopyranosyl(1→6)]-β-d-glucoside (19), and quercetin 3-O-[2-O″-(E)-p-coumaroyl][α-L-rhamnopyranosyl(1→6)]-β-D-glucoside (20), together with caffeine and known catechins, and flavonoids (1-16) were isolated from the leaves of Camellia sinensis. Their structures were determined by spectroscopic (1D and 2D NMR, IR, and HR-TOF-MS) and chemical methods. The catechins and flavonoidal glycosides exhibited yeast alcohol dehydrogenase (ADH) inhibitory activities in the range of IC(50) 8.0-70.3μM, and radical scavenging activities in the range of IC(50) 1.5-43.8 μM, measured by using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS

PubMed Central

Yoo, Chul; Patwa, Tasneem H.; Kreunin, Paweena; Miller, Fred R.; Huber, Christian G.; Nesvizhskii, Alexey I.; Lubman, David M.

2012-01-01

A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 μg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis. PMID:17206599

Quantitative detection of RO2 radicals and other products from cyclohexene ozonolysis with ammonium-CI3-TOF and acetate-CI-API-TOF

NASA Astrophysics Data System (ADS)

Hansel, A.; Scholz, W.; Mentler, B.; Fischer, L.; Berndt, T.

2017-12-01

The performance of the novel ammonium-CI3-TOF utilizing NH4+ adduct ion chemistry to measure quantitatively first generation oxidized product molecules (OMs) as well as highly oxidized organic molecules (HOMs) was investigated for the first time. The gas-phase ozonolysis of cyclohexene served as a test system in order to evaluate the capability of the detection systems. Experiments have been carried out in the TROPOS free-jet flow system at close to atmospheric conditions. Product ion signals were simultaneously observed by the ammonium-CI3-TOF and the acetate-CI-API-TOF. Both instruments are in remarkable good agreement within a factor of two for HOMs. For OMs not containing an OOH group the acetate technique can considerably underestimate OM concentrations by 2-3 orders of magnitude. First steps of cyclohexene ozonolysis generate ten different (m/z product peaks) main products comprising 92% of observed OMs. The remaining 8% are distributed over several (m/z peaks) minor products that can be attributed to HOMs, predominately to highly oxidized RO2 radicals. Summing up, observed ammonium-CI3-TOF products yield 4.9 x 109 molecules cm-³ in excellent agreement with the amount of reacted cyclohexene of 5.0 x 109 molecules cm-³ for reactant concentrations of [O3] = 2.25 x 1012 molecules cm-³ and [cyclohexene] = 2.0 x 1012 molecules cm-³ and a reaction time of 7.9 s. NH4+ adduct ion chemistry based CIMS techniques offer a unique opportunity for complete detection of the whole product distribution, and consequently, for a much better understanding of atmospheric oxidation processes.

Phosphorylation of CMG helicase and Tof1 is required for programmed fork arrest

PubMed Central

Bastia, Deepak; Srivastava, Pankaj; Zaman, Shamsu; Choudhury, Malay; Mohanty, Bidyut K.; Bacal, Julien; Langston, Lance D.; Pasero, Philippe; O’Donnell, Michael E.

2016-01-01

Several important physiological transactions, including control of replicative life span (RLS), prevention of collision between replication and transcription, and cellular differentiation, require programmed replication fork arrest (PFA). However, a general mechanism of PFA has remained elusive. We previously showed that the Tof1–Csm3 fork protection complex is essential for PFA by antagonizing the Rrm3 helicase that displaces nonhistone protein barriers that impede fork progression. Here we show that mutations of Dbf4-dependent kinase (DDK) of Saccharomyces cerevisiae, but not other DNA replication factors, greatly reduced PFA at replication fork barriers in the spacer regions of the ribosomal DNA array. A key target of DDK is the mini chromosome maintenance (Mcm) 2–7 complex, which is known to require phosphorylation by DDK to form an active CMG [Cdc45 (cell division cycle gene 45), Mcm2–7, GINS (Go, Ichi, Ni, and San)] helicase. In vivo experiments showed that mutational inactivation of DDK caused release of Tof1 from the chromatin fractions. In vitro binding experiments confirmed that CMG and/or Mcm2–7 had to be phosphorylated for binding to phospho-Tof1–Csm3 but not to its dephosphorylated form. Suppressor mutations that bypass the requirement for Mcm2–7 phosphorylation by DDK restored PFA in the absence of the kinase. Retention of Tof1 in the chromatin fraction and PFA in vivo was promoted by the suppressor mcm5-bob1, which bypassed DDK requirement, indicating that under this condition a kinase other than DDK catalyzed the phosphorylation of Tof1. We propose that phosphorylation regulates the recruitment and retention of Tof1–Csm3 by the replisome and that this complex antagonizes the Rrm3 helicase, thereby promoting PFA, by preserving the integrity of the Fob1–Ter complex. PMID:27298353

[Molecular characterization of pathogenic bacteria of the respiratory tract in peruvian patients with cystic fibrosis].

PubMed

Aquino, Ruth; Gonzáles, Emely; Samaniego, Sol; Rivera, Juan; Cedeño, Virna; Urbina, Yrene; Diringer, Benoit

2017-01-01

To molecularly characterize the pathogenic bacteria of the respiratory tract isolated from patients with cystic fibrosis (CF) in Peru. Bacterial communities cultured from sputum samples of pediatric and adult patients with CF admitted to the Edgardo Rebagliati Martins National Hospital and the National Institute of Child Health were characterized. Standard microbiological techniques were used for bacterial culture, and gene sequencing of 16S rRNA and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and tandem MALDI-TOF mass spectrometry (MALDI TOF/TOF) were used for molecular characterization. Seventeen bacterial strains were characterized by 16S rRNA sequencing, and the identified pathogenic bacteria were Pseudomonas aeruginosa (31.5%), Staphylococcus aureus (12.6%), Pseudomonas spp. (11.8%), and Klebsiella oxytoca (3.1%). MALDI-TOF analysis generated a series of spectra representative of each isolated bacterial species, whereas MALDI TOF/TOF analysis identified the peptides and proteins of the most common strains and provided data on pathogenicity and sensitivity to antibiotics. The primary pathogenic microorganisms found in the respiratory tract of patients with CF in Peru were the same as those found in other countries. This study is the first to perform 16S rRNA sequencing as well as MALDI-TOF and MALDI-TOF/TOF analysis of the bacterial pathogens circulating in Peru. The inclusion of proteomic analysis further allowed for the identification of native microorganisms involved in CF.

Non-Enhanced MR Imaging of Cerebral Arteriovenous Malformations at 7 Tesla.

PubMed

Wrede, Karsten H; Dammann, Philipp; Johst, Sören; Mönninghoff, Christoph; Schlamann, Marc; Maderwald, Stefan; Sandalcioglu, I Erol; Ladd, Mark E; Forsting, Michael; Sure, Ulrich; Umutlu, Lale

2016-03-01

To evaluate prospectively 7 Tesla time-of-flight (TOF) magnetic resonance angiography (MRA) and 7 Tesla non-contrast-enhanced magnetization-prepared rapid acquisition gradient-echo (MPRAGE) for delineation of intracerebral arteriovenous malformations (AVMs) in comparison to 1.5 Tesla TOF MRA and digital subtraction angiography (DSA). Twenty patients with single or multifocal AVMs were enrolled in this trial. The study protocol comprised 1.5 and 7 Tesla TOF MRA and 7 Tesla non-contrast-enhanced MPRAGE sequences. All patients underwent an additional four-vessel 3D DSA. Image analysis of the following five AVM features was performed individually by two radiologists on a five-point scale: nidus, feeder(s), draining vein(s), relationship to adjacent vessels, and overall image quality and presence of artefacts. A total of 21 intracerebral AVMs were detected. Both sequences at 7 Tesla were rated superior over 1.5 Tesla TOF MRA in the assessment of all considered AVM features. Image quality at 7 Tesla was comparable with DSA considering both sequences. Inter-observer accordance was good to excellent for the majority of ratings. This study demonstrates excellent image quality for depiction of intracerebral AVMs using non-contrast-enhanced 7 Tesla MRA, comparable with DSA. Assessment of untreated AVMs is a promising clinical application of ultra-high-field MRA. • Non-contrast-enhanced 7 Tesla MRA demonstrates excellent image quality for intracerebral AVM depiction. • Image quality at 7 Tesla was comparable with DSA considering both sequences. • Assessment of intracerebral AVMs is a promising clinical application of ultra-high-field MRA.

Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging

DTIC Science & Technology

2009-10-01

molecular breast imaging, with the ability to dynamically contour any sized breast, will improve detection and potentially in vivo characterization of...Having flexible 3D positioning about the breast yielded minimal RMSD differences, which is important for high resolution molecular emission imaging. This...TITLE: Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging PRINCIPAL

The subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3: dynamics and interdependence

PubMed Central

2014-01-01

Background The S-phase checkpoint aims to prevent cells from generation of extensive single-stranded DNA that predisposes to genome instability. The S. cerevisiae complex Tof1/Csm3/Mrc1 acts to restrain the replicative MCM helicase when DNA synthesis is prohibited. Keeping the replication machinery intact allows restart of the replication fork when the block is relieved. Although the subunits of the Tof1/Csm3/Mrc1 complex are well studied, the impact of every single subunit on the triple complex formation and function needs to be established. Findings This work studies the cellular localization and the chromatin binding of GFP-tagged subunits when the complex is intact and when a subunit is missing. We demonstrate that the complex is formed in cell nucleus, not the cytoplasm, as Tof1, Csm3 and Mrc1 enter the nucleus independently from one another. Via in situ chromatin binding assay we show that a Tof1-Csm3 dimer formation and chromatin binding is required to ensure the attachment of Mrc1 to chromatin. Our study indicates that the translocation into the nucleus is not the process to regulate the timing of chromatin association of Mrc1. We also studied the nuclear behavior of Mrc1 subunit in the process of adaptation to the presence hydroxyurea. Our results indicate that after prolonged HU incubation, cells bypass the S-phase checkpoint and proceed throughout the cell cycle. This process is accompanied by Mrc1 chromatin detachment and Rad53 dephosphorylation. Conclusions In S. cerevisiae the subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3 independently enter the cell nucleus, where a Tof1-Csm3 dimer is formed to ensure the chromatin binding of Mrc1 and favor DNA replication and S-phase checkpoint fork arrest. In the process of adaptation to the presence of hydroxyurea Mrc1 is detached from chromatin and Rad53 checkpoint activity is diminished in order to allow S-phase checkpoint escape and completion of the cell cycle. PMID:25379053

The subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3: dynamics and interdependence.

PubMed

Uzunova, Sonya Dimitrova; Zarkov, Alexander Stefanov; Ivanova, Anna Marianova; Stoynov, Stoyno Stefanov; Nedelcheva-Veleva, Marina Nedelcheva

2014-01-01

The S-phase checkpoint aims to prevent cells from generation of extensive single-stranded DNA that predisposes to genome instability. The S. cerevisiae complex Tof1/Csm3/Mrc1 acts to restrain the replicative MCM helicase when DNA synthesis is prohibited. Keeping the replication machinery intact allows restart of the replication fork when the block is relieved. Although the subunits of the Tof1/Csm3/Mrc1 complex are well studied, the impact of every single subunit on the triple complex formation and function needs to be established. This work studies the cellular localization and the chromatin binding of GFP-tagged subunits when the complex is intact and when a subunit is missing. We demonstrate that the complex is formed in cell nucleus, not the cytoplasm, as Tof1, Csm3 and Mrc1 enter the nucleus independently from one another. Via in situ chromatin binding assay we show that a Tof1-Csm3 dimer formation and chromatin binding is required to ensure the attachment of Mrc1 to chromatin. Our study indicates that the translocation into the nucleus is not the process to regulate the timing of chromatin association of Mrc1. We also studied the nuclear behavior of Mrc1 subunit in the process of adaptation to the presence hydroxyurea. Our results indicate that after prolonged HU incubation, cells bypass the S-phase checkpoint and proceed throughout the cell cycle. This process is accompanied by Mrc1 chromatin detachment and Rad53 dephosphorylation. In S. cerevisiae the subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3 independently enter the cell nucleus, where a Tof1-Csm3 dimer is formed to ensure the chromatin binding of Mrc1 and favor DNA replication and S-phase checkpoint fork arrest. In the process of adaptation to the presence of hydroxyurea Mrc1 is detached from chromatin and Rad53 checkpoint activity is diminished in order to allow S-phase checkpoint escape and completion of the cell cycle.

A New Approach for Combining Time-of-Flight and RGB Cameras Based on Depth-Dependent Planar Projective Transformations

PubMed Central

Salinas, Carlota; Fernández, Roemi; Montes, Héctor; Armada, Manuel

2015-01-01

Image registration for sensor fusion is a valuable technique to acquire 3D and colour information for a scene. Nevertheless, this process normally relies on feature-matching techniques, which is a drawback for combining sensors that are not able to deliver common features. The combination of ToF and RGB cameras is an instance that problem. Typically, the fusion of these sensors is based on the extrinsic parameter computation of the coordinate transformation between the two cameras. This leads to a loss of colour information because of the low resolution of the ToF camera, and sophisticated algorithms are required to minimize this issue. This work proposes a method for sensor registration with non-common features and that avoids the loss of colour information. The depth information is used as a virtual feature for estimating a depth-dependent homography lookup table (Hlut). The homographies are computed within sets of ground control points of 104 images. Since the distance from the control points to the ToF camera are known, the working distance of each element on the Hlut is estimated. Finally, two series of experimental tests have been carried out in order to validate the capabilities of the proposed method. PMID:26404315

Rapid Identification of Microorganisms from Positive Blood Culture by MALDI-TOF MS After Short-Term Incubation on Solid Medium.

PubMed

Curtoni, Antonio; Cipriani, Raffaella; Marra, Elisa Simona; Barbui, Anna Maria; Cavallo, Rossana; Costa, Cristina

2017-01-01

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms. Unfortunately, its direct application to positive blood culture is still lacking standardized procedures. In this study, we evaluated an easy- and rapid-to-perform protocol for MALDI-TOF MS direct identification of microorganisms from positive blood culture after a short-term incubation on solid medium. This protocol was used to evaluate direct identification of microorganisms from 162 positive monomicrobial blood cultures; at different incubation times (3, 5, 24 h), MALDI-TOF MS assay was performed from the growing microorganism patina. Overall, MALDI-TOF MS concordance with conventional methods at species level was 60.5, 80.2, and 93.8% at 3, 5, and 24 h, respectively. Considering only bacteria, the identification performances at species level were 64.1, 85.0, and 94.1% at 3, 5, and 24 h, respectively. This protocol applied to a commercially available MS typing system may represent, a fast and powerful diagnostic tool for pathogen direct identification and for a promptly and pathogen-driven antimicrobial therapy in selected cases.

Investigation of Fully Three-Dimensional Helical RF Field Effects on TWT Beam/Circuit Interaction

NASA Technical Reports Server (NTRS)

Kory, Carol L.

2000-01-01

A fully three-dimensional (3D), time-dependent, helical traveling wave-tube (TWT) interaction model has been developed using the electromagnetic particle-in-cell (PIC) code MAFIA. The model includes a short section of helical slow-wave circuit with excitation fed by RF input/output couplers, and electron beam contained by periodic permanent magnet (PPM) focusing. All components of the model are simulated in three dimensions allowing the effects of the fully 3D helical fields on RF circuit/beam interaction to be investigated for the first time. The development of the interaction model is presented, and predicted TWT performance using 2.5D and 3D models is compared to investigate the effect of conventional approximations used in TWT analyses.

Using Secondary Nuclear Reaction Products to Infer the Fuel Areal Density, Convergence, and Electron Temperatures of Imploding D2 and D3 He Filled Capsules on the NIF

NASA Astrophysics Data System (ADS)

Lahmann, B.; Frenje, J. A.; Gatu Johnson, M.; Seguin, F. H.; Li, C. K.; Petrasso, R. D.; Hartouni, E. P.; Yeamans, C. B.; Rinderknecht, H. G.; Sayre, D. B.; Grim, G.; Baker, K.; Casey, D. T.; Dewald, E.; Goyon, C.; Jarrott, L. C.; Khan, S.; Lepape, S.; Ma, T.; Pickworth, L.; Shah, R.; Kline, J. L.; Perry, T.; Zylstra, A.; Yi, S. A.

2017-10-01

In deuterium-filled inertial confinement fusion implosions, 0.82 MeV 3He and 1.01 MeV T (generated by the primary DD reaction branches) can undergo fusion reactions with the thermal deuterium plasma to create secondary D3He protons and DT neutrons, respectively. In regimes of moderate fuel areal density (ρR 5 - 100 mg/cm2) the ratio of both of these secondary yields to the primary yield can be used to infer the fuel ρR, convergence ratio (CR), and an electron temperature (Te) . This technique has been used on a myriad of deuterium filled capsule implosion experiments on the NIF using the neutron time of flight (nTOF) diagnostics to measure the yield of secondary DT neutrons and CR-39 based wedge range filters (WRFs) to measure the yield of secondary D3He protons. This work is supported in part by the U.S. DoE and LLNL.

Research on online 3D laser scanner dimensional measurement system for heavy high-temperature forgings

NASA Astrophysics Data System (ADS)

Zhu, Jingguo; Li, Menglin; Jiang, Yan; Xie, Tianpeng; Li, Feng; Jiang, Chenghao; Liu, Ruqing; Meng, Zhe

2017-10-01

Online 3-D laser-scanner is a non-contact measurement system with high speed, high precision and easy operation, which can be used to measure heavy and high-temperature forgings. But the current online laser measurement system is mainly a mobile light indicator, which can only be used in the limited environment and lacks the capability of 3-D accurate measurement. This paper mainly introduces the structure of the online high-speed real-time 3-D measurement for heavy high-temperature forgings of Academy of Opto-Electronics (AOE), Chinese Academy of Sciences. Combining TOF pulse distance measurement with hybrid scan mode, the system can scan and acquire point cloud data of an area of 20m×10m with a 75°×40° field of view at the distance of 20m. The entire scanning time is less than 5 seconds with an accuracy of 8mm, which can meet the online dimensional measurement requirements of heavy high-temperature forgings.

Complete Versus Staged Repair for Neonates With Tetralogy of Fallot: Establishment and Validation of a Cohort of 2235 Patients Using Detailed Surgery Sequence Review of Health Care Administrative Data.

PubMed

Savla, Jill J; Fisher, Brian T; Faerber, Jennifer A; Huang, Yuan-Shung V; Mercer-Rosa, Laura

2017-12-12

The surgical strategy for neonates with tetralogy of Fallot (TOF) consists of complete or staged repair. Assessing the comparative effectiveness of these approaches is facilitated by a large multicenter cohort. We propose a novel process for cohort assembly using the Pediatric Health Information System (PHIS), an administrative database that contains clinical and billing data for inpatient and emergency department stays from tertiary children's hospitals. A 4-step process was used to identify neonates with TOF: (1) screen neonates in PHIS with International Classification of Diseases-9 (ICD-9) diagnosis or procedure codes for TOF; (2) include patients with TOF procedures before 30 days of age; (3) exclude patients with missing 2-year follow-up data; (4) analyze patients' 2-year surgery sequence patterns, exclude patients inconsistent with a treatment strategy for TOF, and designate patients as complete or staged repair. Manual chart review at 1 PHIS center was performed to validate this process. Between January 2004 and March 2015, 5862 patients were identified in step 1. Step 2 of cohort assembly excluded 3425 patients (58%); step 3 excluded 148 patients (3%); and step 4 excluded 54 patients (1%). The final cohort consisted of 2235 neonates with TOF from 45 hospitals. Manual chart review of 336 patients showed a positive predictive value for accurate PHIS identification of 44% after step 1 and 97% after step 4. This systematic cohort identification algorithm resulted in a high positive predictive value to appropriately categorize patients. This carefully assembled cohort offers a unique opportunity for future studies in neonatal TOF outcomes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Xiangmei; Mort, Andrew

A comore » mmercial apple pectin was sequentially digested with the cloned enzymes endopolygalacturonase, galactanase, arabinofuranosidase, xylogalacturonase, and rhamnogalacturonan hydrolase. The rhamnogalacturonan hydrolase-generated oligosaccharides were separated by ultrafiltration, anion exchange, and size-exclusion chromatography. Fractions from the ion exchange chromatography were pooled, lyophilized, and screened by MALDI-TOF MS. An oligosaccharide (RGP14P3) was identified and its structure, α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A, determined by 1D and 2D NMR spectrometry. This oligosaccharide probably represents a direct connection between homogalacturonan and rhamnogalacturonan in pectin. Alternatively, it could indicate that the nonreducing end of rhamnogalacturonan starts with a galacturonic acid residue.« less

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens.

PubMed

Huang, Yanfei; Wang, Jinglin; Zhang, Mingxin; Zhu, Min; Wang, Mei; Sun, Yufeng; Gu, Haitong; Cao, Jingjing; Li, Xue; Zhang, Shaoya; Lu, Xinxin

2017-03-01

Filamentous fungi are among the most important pathogens, causing fungal rhinosinusitis (FRS). Current laboratory diagnosis of FRS pathogens mainly relies on phenotypic identification by culture and microscopic examination, which is time consuming and expertise dependent. Although matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS has been employed to identify various fungi, its efficacy in the identification of FRS fungi is less clear. A total of 153 FRS isolates obtained from patients were analysed at the Clinical Laboratory at the Beijing Tongren Hospital affiliated to the Capital Medical University, between January 2014 and December 2015. They were identified by traditional phenotypic methods and Bruker MALDI-TOF MS (Bruker, Biotyper version 3.1), respectively. Discrepancies between the two methods were further validated by sequencing. Among the 153 isolates, 151 had correct species identification using MALDI-TOF MS (Bruker, Biot 3.1, score ≥2.0 or 2.3). MALDI-TOF MS enabled identification of some very closely related species that were indistinguishable by conventional phenotypic methods, including 1/10 Aspergillus versicolor, 3/20 Aspergillus flavus, 2/30 Aspergillus fumigatus and 1/20 Aspergillus terreus, which were misidentified by conventional phenotypic methods as Aspergillus nidulans, Aspergillus oryzae, Aspergillus japonicus and Aspergillus nidulans, respectively. In addition, 2/2 Rhizopus oryzae and 1/1 Rhizopus stolonifer that were identified only to the genus level by the phenotypic method were correctly identified by MALDI-TOF MS. MALDI-TOF MS is a rapid and accurate technique, and could replace the conventional phenotypic method for routine identification of FRS fungi in clinical microbiology laboratories.

A new retrospective, multi-evidence veterinary drug screening method using drift tube ion mobility mass spectrometry.

PubMed

Xu, Zhenzhen; Li, Jianzhong; Chen, Ailiang; Ma, Xin; Yang, Shuming

2018-05-03

The retrospectivity (the ability to retrospect to a previously unknown compound in raw data) is very meaningful for food safety and risk assessment when facing new emerging drugs. Accurate mass and retention time based screening may lead false positive and false negative results so new retrospective, reliable platform is desirable. Different concentration levels of standards with and without matrix were analyzed using ion mobility (IM)-quadrupole-time-of-flight (Q-TOF) for collecting retrospective accurate mass, retention time, drift time and tandem MS evidence for identification in a single experiment. The isomer separation ability of IM and the four-dimensional (4D) feature abundance quantification abilities were evaluated for veterinary drugs for the first time. The sensitivity of the IM-Q-TOF workflow was obviously higher than that of the traditional database searching algorithm [find by formula (FbF) function] for Q-TOF. In addition, the IM-Q-TOF workflow contained most of the results from FbF and removed the false positive results. Some isomers were separated by IM and the 4D feature abundance quantitation removed interference with similar accurate mass and showed good linearity. A new retrospective, multi-evidence platform was built for veterinary drug screening in a single experiment. The sensitivity was significantly improved and the data can be used for quantification. The platform showed its potential to be used for food safety and risk assessment. This article is protected by copyright. All rights reserved.

High-speed digitization readout of silicon photomultipliers for time of flight positron emission tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronzhin, A.; Los, S.; Martens, M.

2011-02-01

We report on work to develop a system with about 100 picoseconds (ps) time resolution for time of flight positron emission tomography [TOF-PET]. The chosen photo detectors for the study were Silicon Photomultipliers (SiPM's). This study was based on extensive experience in studying timing properties of SiPM's. The readout of these devices used the commercial high speed digitizer DRS4. We applied different algorithms to get the best time resolution of 155 ps Guassian (sigma) for a LYSO crystal coupled to a SiPM. We consider the work as a first step in building a prototype TOF-PET module. The field of positron-emission-tomographymore » (PET) has been rapidly developing. But there are significant limitations in how well current PET scanners can reconstruct images, related to how fast data can be acquired, how much volume they can image, and the spatial and temporal resolution of the generated photons. Typical modern scanners now include multiple rings of detectors, which can image a large volume of the patient. In this type of scanner, one can treat each ring as a separate detector and require coincidences only within the ring, or treat the entire region viewed by the scanner as a single 3 dimensional volume. This 3d technique has significantly better sensitivity since more photon pair trajectories are accepted. However, the scattering of photons within the volume of the patient, and the effect of random coincidences limits the technique. The advent of sub-nanosecond timing resolution detectors means that there is potentially much better rejection of scattered photon events and random coincidence events in the 3D technique. In addition, if the timing is good enough, then the origin of photons pairs can be determined better, resulting in improved spatial resolution - so called 'Time-of-Flight' PET, or TOF-PET. Currently a lot of activity has occurred in applications of SiPMs for TOF-PET. This is due to the devices very good time resolution, low profile, lack of high voltage needed, and their non-sensitivity to magnetic fields. While investigations into this technique have begun elsewhere, we feel that the extensive SiPM characterization and data acquisition expertise of Fermilab, and the historical in-depth research of PET imaging at University of Chicago will combine to make significant strides in this field. We also benefit by a working relationship with the SiPM producer STMicroelectronics (STM).« less

Comparison of carotid plaque ulcer detection using contrast-enhanced and time-of-flight MRA techniques.

PubMed

Etesami, M; Hoi, Y; Steinman, D A; Gujar, S K; Nidecker, A E; Astor, B C; Portanova, A; Qiao, Y; Abdalla, W M A; Wasserman, B A

2013-01-01

Ulceration in carotid plaque is a risk indicator for ischemic stroke. Our aim was to compare plaque ulcer detection by standard TOF and CE-MRA techniques and to identify factors that influence its detection. Carotid MR imaging scans were acquired on 2066 participants in the ARIC study. We studied the 600 thickest plaques. TOF-MRA, CE-MRA, and black-blood MR images were analyzed together to define ulcer presence (plaque surface niche ≥2 mm in depth). Sixty ulcerated arteries were detected. These arteries were randomly assigned, along with 40 nonulcerated plaques from the remaining 540, for evaluation of ulcer presence by 2 neuroradiologists. Associations between ulcer detection and ulcer characteristics, including orientation, location, and size, were determined and explored by CFD modeling. One CE-MRA and 3 TOF-MRAs were noninterpretable and excluded. Of 71 ulcers in 56 arteries, readers detected an average of 39 (55%) on both TOF-MRA and CE-MRA, 26.5 (37.5%) only on CE-MRA, and 1 (1.5%) only on TOF-MRA, missing 4.5 (6%) ulcers by both methods. Ulcer detection by TOF-MRA was associated with its orientation (distally pointing versus perpendicular: OR = 5.57 [95% CI, 1.08-28.65]; proximally pointing versus perpendicular: OR = 0.21 [95% CI, 0.14-0.29]); location relative to point of maximum stenosis (distal versus isolevel: OR = 5.17 [95% CI, 2.10-12.70]); and neck-to-depth ratio (OR = 1.96 [95% CI, 1.11-3.45]) after controlling for stenosis and ulcer volume. CE-MRA detects more ulcers than TOF-MRA in carotid plaques. Missed ulcers on TOF-MRA are influenced by ulcer orientation, location relative to point of maximum stenosis, and neck-to-depth ratio.

[Rapid identification of two new isomers in bear bile powder by LC-Q-TOF-MS combined with PCC oxidation].

PubMed

Jian, Long-Hai; Hu, Chun; Yu, Hong; Wang, Ke; Ji, Shen

2013-07-01

A rapid method of Liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) combined with pyridinium chlorochromate (PCC) oxidation has been developed to determine chemical structures of two novel isomers in bear bile powder. Derivatives of ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) were semi-synthesized by PCC oxidation, then were analyzed by LC-Q-TOF-MS. Separation was carried out on a reverse column with the mobile phase of acetonitrile-0.1% formic acid (45:55). The data of Q-TOF-MS was acquired by MS, MS/MS, positive and negative modes. Since UDCA and CDCA were stereochemical isomeric at an alcohol position, two oxidation products were same and have been confirmed by LC-Q-TOF-MS. Other two products were also determined based on the PCC oxidation theory. Samples of bear bile powder were dissolved by methanol and measured by LC-Q-TOF-MS. Two unknown peaks were found and identified by matching their retention times and accurate mass spectra ions with PCC oxidation productS. Finally, the structures of two new bile acids in bear bile powder were confirmed as 3alpha-hydroxy-7-oxo-5beta-cholanic acid, 7alpha-hydroxy-3-oxo-5beta-cholanic acid, respectively.

Cardiovascular autonomic dysfunction and carotid stiffness in adults with repaired tetralogy of Fallot.

PubMed

Novaković, Marko; Prokšelj, Katja; Starc, Vito; Jug, Borut

2017-06-01

Adults after surgical repair of tetralogy of Fallot (ToF) may have impaired vascular and cardiac autonomic function. Thus, we wanted to assess interrelations between heart rate variability (HRV) and heart rate recovery (HRR), as parameters of cardiac autonomic function, and arterial stiffness, as a parameter of vascular function, in adults with repaired ToF as compared to healthy controls. In a case-control study of adults with repaired ToF and healthy age-matched controls we measured: 5-min HRV variability (with time and frequency domain data collected), carotid artery stiffness (through pulse-wave analysis using echo-tracking ultrasound) and post-exercise HRR (cycle ergometer exercise testing). Twenty-five patients with repaired ToF (mean age 38 ± 10 years) and 10 healthy controls (mean age 39 ± 8 years) were included. Selected HRR and HRV (time-domain) parameters, but not arterial stiffness were significantly reduced in adults after ToF repair. Moreover, a strong association between late/slow HRR (after 2, 3 and 4 min) and carotid artery stiffness was detected in ToF patients (r = -0.404, p = 0.045; r = -0.545, p = 0.005 and r = -0.545, p = 0.005, respectively), with statistical significance retained even after adjusting for age, gender, resting heart rate and β-blockers use (r = -0.393, p = 0.024 for HRR after 3 min). Autonomic cardiac function is impaired in patients with repaired ToF, and independently associated with vascular function in adults after ToF repair, but not in age-matched healthy controls. These results might help in introducing new predictors of cardiovascular morbidity in a growing population of adults after surgical repair of ToF.

Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation.

PubMed

Chaze, Thibault; Hornez, Louis; Chambon, Christophe; Haddad, Iman; Vinh, Joelle; Peyrat, Jean-Philippe; Benderitter, Marc; Guipaud, Olivier

2013-07-10

The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes.

Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation

PubMed Central

Chaze, Thibault; Hornez, Louis; Chambon, Christophe; Haddad, Iman; Vinh, Joelle; Peyrat, Jean-Philippe; Benderitter, Marc; Guipaud, Olivier

2013-01-01

The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes. PMID:28250398

Identification and Characterization of Lipopeptides from Bacillus subtilis B1 Against Sapstain Fungus of Rubberwood Through MALDI-TOF-MS and RT-PCR.

PubMed

Sajitha, K L; Dev, Suma Arun; Maria Florence, E J

2016-07-01

Bacillus subtilis is a potent biocontrol agent producing a wide array of antifungal lipopeptides for the inhibition of fungal growth. B. subtilis B1 isolated from market-available compost provided an efficient control of rubberwood sapstain fungus, Lasiodiplodia theobromae. The current study is aimed to identify and characterize the lipopeptides responsible for the biocontrol of rubberwood sapstain fungus by Bacillus subtilis B1. The bacterial whole-cell surface extract from the dual culture of B. subtilis B1 and sapstain fungus (L. theobromae) was analysed using MALDI-TOF-MS. The protonated as well as sodium, potassium adducts of homologues of iturin C, surfactin, bacillomycin D and fengycin A and B were identified and expression of the lipopeptide biosynthetic genes could be confirmed through RT-PCR. This is the first report of mycobacillin and trimethylsilyl derivative of bacilysin during antagonism through MALDI-TOF-MS. MALDI-TOF-MS with RT-PCR offered easy platforms to characterize the antifungal lipopeptides. The identification of antifungal lipopeptides can lead to the formulation of prospective biocontrol by-products which have wide-scale utility.

Evaluation of Comprehensive 2-D Gas Chromatography-Time-Of-Flight Mass Spectrometry for 209 Chlorinated Biphenyl Congeners in Two Chromatographic Runs

EPA Science Inventory

This research evaluates a recently developed comprehensive 2-D GC coupled with a time-of-flight (TOF) mass spectrometer for the potential separation of 209 PCB congeners, using a sequence of 1-D and 2-D chromatographic modes. In two consecutive chromatographic runs, using a 40 m,...

Development of capacitive multiplexing circuit for SiPM-based time-of-flight (TOF) PET detector

NASA Astrophysics Data System (ADS)

Choe, Hyeok-Jun; Choi, Yong; Hu, Wei; Yan, Jianhua; Jung, Jin Ho

2017-04-01

There has been great interest in developing a time-of-flight (TOF) PET to improve the signal-to-noise ratio of PET image relative to that of non-TOF PET. Silicon photomultiplier (SiPM) arrays have attracted attention for use as a fast TOF PET photosensor. Since numerous SiPM arrays are needed to construct a modern human PET, a multiplexing method providing both good timing performance and high channel reduction capability is required to develop a SiPM-based TOF PET. The purpose of this study was to develop a capacitive multiplexing circuit for the SiPM-based TOF PET. The proposed multiplexing circuit was evaluated by measuring the coincidence resolving time (CRT) and the energy resolution as a function of the overvoltage using three different capacitor values of 15, 30, and 51 pF. A flood histogram was also obtained and quantitatively assessed. Experiments were performed using a 4× 4 array of 3× 3 mm2 SiPMs. Regarding the capacitor values, the multiplexing circuit using a smaller capacitor value showed the best timing performance. On the other hand, the energy resolution and flood histogram quality of the multiplexing circuit deteriorated as the capacitor value became smaller. The proposed circuit was able to achieve a CRT of 260+/- 4 ps FWHM and an energy resolution of 17.1 % with a pair of 2× 2× 20 mm3 LYSO crystals using a capacitor value of 30 pF at an overvoltage of 3.0 V. It was also possible to clearly resolve a 6× 6 array of LYSO crystals in the flood histogram using the multiplexing circuit. The experiment results indicate that the proposed capacitive multiplexing circuit is useful to obtain an excellent timing performance and a crystal-resolving capability in the flood histogram with a minimal degradation of the energy resolution, as well as to reduce the number of the readout channels of the SiPM-based TOF PET detector.

Value of speckle tracking for the assessment of right ventricular function in patients operated on for tetralogy of fallot. Comparison with magnetic resonance imaging.

PubMed

Bernard, Yvette; Morel, Mathilde; Descotes-Genon, Vincent; Jehl, Jerome; Meneveau, Nicolas; Schiele, Francois

2014-04-01

Right ventricular (RV) function is a major prognostic factor in patients (pts) with operated tetralogy of Fallot (TOF). We compared the results of RV speckle tracking (two-dimensional [2D] strain) with those of magnetic resonance imaging (MRI) in this setting. At transthoracic echocardiogram (echo), RV fractional area change (RVFAC), tricuspid annular plane systolic excursion (TAPSE), velocity of S-wave at tricuspid annulus with tissue Doppler, and 2D strain (longitudinal maximal systolic strain) were recorded. Their results were compared to RV indexed end-diastolic volume (EDV), indexed end-systolic volume (ESV), and RV ejection fraction (EF) at MRI. Twenty-two pts (16 M) aged 11-62 years (mean 23.2 ± 10.8) were included. Parameters of RV systolic function were as follows: RVFAC = 40 ± 10%, TAPSE = 18 ± 4 mm, S-wave = 10 ± 0.2 cm/sec, and RV EF at MRI = 43 ± 11%. Global RV systolic strain was -15.5 ± 4.2%, free wall strain was -15.1 ± 6.3%, and septal strain was -15.8 ± 3.8% on average for the whole group. Echo indexed RV end-diastolic area correlated with EDV at MRI (r = 0.73), as well as echo indexed RV end-systolic area and ESV at MRI (r = 0.71). Global RV 2D strain correlated well with RV EF at MRI: r = 0.68; P < 0.05, and with ESV at MRI: r = 0.63. Feasibility, intra- and inter-observer reproducibility of 2D strain were adequate. Speckle tracking is a promising method to estimate RV systolic function in pts operated on for TOF. © 2013, Wiley Periodicals, Inc.

Systemic alterations in the metabolome of diabetic NOD mice delineate increased oxidative stress accompanied by reduced inflammation and hypertriglyceremia

PubMed Central

Fahrmann, Johannes; Grapov, Dmitry; Yang, Jun; Hammock, Bruce; Fiehn, Oliver; Bell, Graeme I.

2015-01-01

Nonobese diabetic (NOD) mice are a commonly used model of type 1 diabetes (T1D). However, not all animals will develop overt diabetes despite undergoing similar autoimmune insult. In this study, a comprehensive metabolomic approach, consisting of gas chromatography time-of-flight (GC-TOF) mass spectrometry (MS), ultra-high-performance liquid chromatography-accurate mass quadruple time-of-flight (UHPLC-qTOF) MS and targeted UHPLC-tandem mass spectrometry-based methodologies, was used to capture metabolic alterations in the metabolome and lipidome of plasma from NOD mice progressing or not progressing to T1D. Using this multi-platform approach, we identified >1,000 circulating lipids and metabolites in male and female progressor and nonprogressor animals (n = 71). Statistical and multivariate analyses were used to identify age- and sex-independent metabolic markers, which best differentiated metabolic profiles of progressors and nonprogressors. Key T1D-associated perturbations were related with 1) increases in oxidation products glucono-δ-lactone and galactonic acid and reductions in cysteine, methionine and threonic acid, suggesting increased oxidative stress; 2) reductions in circulating polyunsaturated fatty acids and lipid signaling mediators, most notably arachidonic acid (AA) and AA-derived eicosanoids, implying impaired states of systemic inflammation; 3) elevations in circulating triacylglyercides reflective of hypertriglyceridemia; and 4) reductions in major structural lipids, most notably lysophosphatidylcholines and phosphatidylcholines. Taken together, our results highlight the systemic perturbations that accompany a loss of glycemic control and development of overt T1D. PMID:25852003

A new alkaloid from Portulaca oleracea L. and its antiacetylcholinesterase activity.

PubMed

Xiu, Fen; Li, Xuetao; Zhang, Wenjie; He, Fan; Ying, Xixiang; Stien, Didier

2018-04-18

A new alkaloid, (10E, 12E)-9-ureidooctadeca-10, 12-dienoic acid, named oleraurea (1) and 10 known compounds, p-hydroxybenzaldehyde (2), p-hydroxybenzoic acid (3), p-hydroxyacetophenone (4), benzamide (5), (E)-p-coumaramide (6), (E)-ferulamide (7), soyalkaloid A (8), β-carboline-3-carboxylic acid (9), 2, 3, 4, 9-tetrahydro-1H-pyrido [3, 4-b] indole-3-carboxylic acid (10), (1S, 3S)-1-methyl-1, 2, 3, 4-tetrahydro-β-carboline-3-carboxylic acid (11) were obtained from Portulaca oleracea L., in which, compounds 4, 5, 8-11 were isolated from the plant for the first time. The structure of the compound 1 was identified using spectroscopic methods including 1D and 2D NMR, HR-ESI-TOF-MS. The compounds 1, 5-11 presented anticholinesterase activities, but the P. oleracea extract (POE) presented very low anticholinesterase activity.

Insights in the analytical performance of neat metal-organic frameworks in the determination of pollutants of different nature from waters using dispersive miniaturized solid-phase extraction and liquid chromatography.

PubMed

Rocío-Bautista, Priscilla; Pino, Verónica; Pasán, Jorge; López-Hernández, Irene; Ayala, Juan H; Ruiz-Pérez, Catalina; Afonso, Ana M

2018-03-01

Five metal-organic frameworks (MOFs), specifically HKUST-1, MOF-5(Zn), MIL-53(Al), UiO-64 and MOF-74(Zn) are synthesized, characterized, and utilized in a miniaturized solid-phase extraction method under dispersive mode (D-µSPE) for the determination of six pollutants of different nature, including one polycyclic aromatic hydrocarbon, two hormones, two drugs, and one disinfectant, from environmental waters (tap water and wastewater). A discussion of possible interactions justifying the partitioning of target analytes to the MOFs is included, considering not only the analytes' physicochemical characteristics but also those of MOFs: metal nature, structural environment of MOF pores, pore size and pore aperture widths, among others. MIL-53(Al) is selected for its versatility and high extraction efficiency for the target compounds. The D-µSPE method using MIL-53(Al) is optimized and used in combination with high-performance liquid chromatography (HPLC) with diode array detector (DAD) or liquid-chromatography with time-of-flight mass spectrometric detector (LC-TOF). Under optimum conditions, only 5mg of MIL-53(Al) are required for 10mL of water, with the aid of 5min of vortex and 5min of centrifugation. Elution is accomplished with 200µL of acetonitrile (3 times), and evaporation down to 100µL before LC injection. Detection limits down to 0.040μgL -1 for triclosan and 0.013μgL -1 for atrazine are obtained for the entire method using HPLC-DAD and LC-TOF, respectively. The method, operating at low spiked levels (2µgL -1 for HPLC-DAD and 0.7µgL -1 for LC-TOF), is also characterized for average relative recoveries of 109% and 105%; relative standard deviation values lower than 8.7% and 7.5%; and average extraction efficiencies of 41.2% and 49.1%; using HPLC-DAD and LC-TOF, respectively; while demonstrating adequate analytical performance with complex samples such as wastewaters. Copyright © 2017 Elsevier B.V. All rights reserved.

3D lens-free time-lapse microscopy for 3D cell culture

NASA Astrophysics Data System (ADS)

Berdeu, Anthony; Momey, Fabien; Laperrousaz, Bastien; Bordy, Thomas; Gidrol, Xavier; Dinten, Jean-Marc; Picollet-D'hahan, Nathalie; Allier, Cédric

2017-07-01

We propose a new imaging platform based on lens-free time-lapse microscopy for 3D cell culture and its dedicated algorithm lying on a fully 3D regularized inverse problem approach. First 3D+t results are presented

Objective and subjective comparison of standard 2-D and fully 3-D reconstructed data on a PET/CT system.

PubMed

Strobel, Klaus; Rüdy, Matthias; Treyer, Valerie; Veit-Haibach, Patrick; Burger, Cyrill; Hany, Thomas F

2007-07-01

The relative advantage of fully 3-D versus 2-D mode for whole-body imaging is currently the focus of considerable expert debate. The nature of 3-D PET acquisition for FDG PET/CT theoretically allows a shorter scan time and improved efficiency of FDG use than in the standard 2-D acquisition. We therefore objectively and subjectively compared standard 2-D and fully 3-D reconstructed data for FDG PET/CT on a research PET/CT system. In a total of 36 patients (mean 58.9 years, range 17.3-78.9 years; 21 male, 15 female) referred for known or suspected malignancy, FDG PET/CT was performed using a research PET/CT system with advanced detector technology with improved sensitivity and spatial resolution. After 45 min uptake, a low-dose CT (40 mAs) from head to thigh was performed followed by 2-D PET (emission 3 min per field) and 3-D PET (emission 1.5 min per field) with both seven slices overlap to cover the identical anatomical region. Acquisition time was therefore 50% less (seven fields; 21 min vs. 10.5 min). PET data was acquired in a randomized fashion, so in 50% of the cases 2-D data was acquired first. CT data was used for attenuation correction. 2-D (OSEM) and 3-D PET images were iteratively reconstructed. Subjective analysis of 2-D and 3-D images was performed by two readers in a blinded, randomized fashion evaluating the following criteria: sharpness of organs (liver, chest wall/lung), overall image quality and detectability and dignity of each identified lesion. Objective analysis of PET data was investigated measuring maximum standard uptake value with lean body mass (SUV(max,LBM)) of identified lesions. On average, per patient, the SUV(max) was 7.86 (SD 7.79) for 2-D and 6.96 (SD 5.19) for 3-D. On a lesion basis, the average SUV(max) was 7.65 (SD 7.79) for 2-D and 6.75 (SD 5.89) for 3-D. The absolute difference on a paired t-test of SUV 3-D-2-D based on each measured lesion was significant with an average of -0.956 (P=0.002) and an average of -0.884 on a patient base (P<0.05). With 3-D the SUV(max) decreased by an average of 5.2% for each lesion, and an average of 6.0% for each patient. Subjective analysis showed fair inter-observer agreement regarding detectability (kappa=0.24 for 3-D; 0.36 for 3-D) and dignity (kappa=0.44 for 3-D and 0.4 for 2-D) of the lesions. There was no significant diagnostic difference between 3-D and 2-D. Only in one patient, a satellite liver metastasis of a colon cancer was missed in 3-D and detected only in 2-D. On average, the overall image quality for 3-D images was equal (in 24%) or inferior (in 76%) compared to 2-D. A possible major advantage of 3-D data acquisition is the faster patient throughput with a 50% reduction in scan time. The fully 3-D reconstruction technique has overcome the technical drawbacks of current 3-D imaging technique. In our limited number of patients there was no significant diagnostic difference between 2-D and fully 3-D.

Approximating the Probability of Mortality Due to Protracted Radiation Exposures

DTIC Science & Technology

2016-06-01

syndrome of acute radiation sickness. In the MARCELL model, radiation exposure dynamically depletes the bone marrow cell population, the underpinning of...Protracted Radiation Exposures DTRA-TR-16-054 HDTRA1-14-D-0003; 0005 Prepared by: Applied Research Associates, Inc. 801 N. Quincy Street...Celsius (oC) degree Fahrenheit (oF) [T(oF) + 459.67]/1.8 kelvin (K) Radiation curie (Ci) [activity of radionuclides] 3.7 × 1010 per second (s–1

Identification of avocado (Persea americana) root proteins induced by infection with the oomycete Phytophthora cinnamomi using a proteomic approach.

PubMed

Acosta-Muñiz, Carlos H; Escobar-Tovar, Lina; Valdes-Rodríguez, Silvia; Fernández-Pavia, Silvia; Arias-Saucedo, Luis J; de la Cruz Espindola Barquera, Maria; Gómez Lim, Miguel Á

2012-01-01

Avocado root rot, caused by Phytophthora cinnamomi, is the most important disease that limits avocado production. A proteomic approach was employed to identify proteins that are upregulated by infection with P. cinnamomi. Different proteins were shown to be differentially expressed after challenge with the pathogen by two-dimensional (2-D) gel electrophoresis. A densitometric evaluation of protein expression indicated differential regulation during the time-course analyzed. Some proteins induced in response to the infection were identified by standard peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry and sequencing by MALDI LIFT-TOF/TOF tandem mass spectrometry. Of the 400 protein spots detected on 2-D gels, 21 seemed to change in abundance by 3 hours after infection. Sixteen proteins were upregulated, 5 of these were only detected in infected roots and 11 showed an increased abundance. Among the differentially expressed proteins identified are homologs to isoflavone reductase, glutathione S-transferase, several abscisic acid stress-ripening proteins, cinnamyl alcohol dehydrogenase, cinnamoyl-CoA reductase, cysteine synthase and quinone reductase. A 17.3-kDa small heat-shock protein and a glycine-rich RNA-binding protein were identified as downregulated. Our group is the first to report on gene induction in response to oomycete infection in roots from avocado, using proteomic techniques. Copyright © Physiologia Plantarum 2011.

Usefulness of the advanced neuroimaging protocol based on plain and gadolinium-enhanced constructive interference in steady state images for gamma knife radiosurgery and planning microsurgical procedures for skull base tumors.

PubMed

Hayashi, Motohiro; Chernov, Mikhail F; Tamura, Noriko; Yomo, Shoji; Tamura, Manabu; Horiba, Ayako; Izawa, Masahiro; Muragaki, Yoshihiro; Iseki, Hiroshi; Okada, Yoshikazu; Ivanov, Pavel; Régis, Jean; Takakura, Kintomo

2013-01-01

Gamma Knife radiosurgery (GKS) is currently performed with 0.1 mm preciseness, which can be designated microradiosurgery. It requires advanced methods for visualizing the target, which can be effectively attained by a neuroimaging protocol based on plain and gadolinium-enhanced constructive interference in steady state (CISS) images. Since 2003, the following thin-sliced images are routinely obtained before GKS of skull base lesions in our practice: axial CISS, gadolinium-enhanced axial CISS, gadolinium-enhanced axial modified time-of-flight (TOF), and axial computed tomography (CT). Fusion of "bone window" CT and magnetic resonance imaging (MRI), and detailed three-dimensional (3D) delineation of the anatomical structures are performed with the Leksell GammaPlan (Elekta Instruments AB). Recently, a similar technique has been also applied to evaluate neuroanatomy before open microsurgical procedures. Plain CISS images permit clear visualization of the cranial nerves in the subarachnoid space. Gadolinium-enhanced CISS images make the tumor "lucid" but do not affect the signal intensity of the cranial nerves, so they can be clearly delineated in the vicinity to the lesion. Gadolinium-enhanced TOF images are useful for 3D evaluation of the interrelations between the neoplasm and adjacent vessels. Fusion of "bone window" CT and MRI scans permits simultaneous assessment of both soft tissue and bone structures and allows 3D estimation and correction of MRI distortion artifacts. Detailed understanding of the neuroanatomy based on application of the advanced neuroimaging protocol permits performance of highly conformal and selective radiosurgical treatment. It also allows precise planning of the microsurgical procedures for skull base tumors.

Time-of-flight magnetic resonance angiography (TOF-MRA) of the normal equine head.

PubMed

Manso-Díaz, G; García-Real, M I; Casteleyn, C; San-Román, F; Taeymans, O

2013-03-01

Noncontrast magnetic resonance angiography (MRA) is widely used in human and small animal medicine. However, this technique has not yet been described in the horse, and compared to other angiographic techniques MRA could be more cost efficient and potentially safer. The aim of this study was to provide a comprehensive anatomical reference of the normal equine head vasculature using a noncontrast MRA technique, on both low- and high-field MRI. Five healthy adult horses were examined, 4 with a low-field magnet (0.23T) and the remaining one with a high-field magnet (1.5T). The magnetic resonance angiography sequence used was TOF (time-of-flight) 2D-MRA and CT images of a vascular corrosion cast were subsequently used as anatomical references. The MRA imaging protocol provided good visualisation of all major intra- and extracranial vessels down to a size of approximately 2 mm in diameter on both low- and high-field systems. This resulted in identification of vessels to the order of 3rd-4th branches of ramification. The visibility of the arteries was higher than of the veins, which showed lower signal intensity. Overall, MRA obtained with the high-field protocol provided better visualisation of the arteries, showing all the small arterial branches with a superior resolution. The use of a specific vascular sequence such as TOF 2D-MRA allows good visualisation of the equine head vasculature and eliminates the need for contrast media for MRA. Magnetic resonance angiography allows for visualisation of the vasculature of the equine head. Vessel morphology, symmetry and size can be evaluated and this may possibly play a role in preoperative planning or characterisation of diseases of the head, such as neoplasia or guttural pouch mycosis. © 2012 EVJ Ltd.

Quantitative phase analysis of challenging samples using neutron powder diffraction. Sample #4 from the CPD QPA round robin revisited

DOE PAGES

Whitfield, Pamela S.

2016-04-29

Here, quantitative phase analysis (QPA) using neutron powder diffraction more often than not involves non-ambient studies where no sample preparation is possible. The larger samples and penetration of neutrons versus X-rays makes neutron diffraction less susceptible to inhomogeneity and large grain sizes, but most well-characterized QPA standard samples do not have these characteristics. Sample #4 from the International Union of Crystallography Commission on Powder Diffraction QPA round robin was one such sample. Data were collected using the POWGEN time-of-flight (TOF) neutron powder diffractometer and analysed together with historical data from the C2 diffractometer at Chalk River. The presence of magneticmore » reflections from Fe 3O 4 (magnetite) in the sample was an additional consideration, and given the frequency at which iron-containing and other magnetic compounds are present during in-operando studies their possible impact on the accuracy of QPA is of interest. Additionally, scattering from thermal diffuse scattering in the high-Qregion (<0.6 Å) accessible with TOF data could impact QPA results during least-squares because of the extreme peak overlaps present in this region. Refinement of POWGEN data was largely insensitive to the modification of longer d-spacing reflections by magnetic contributions, but the constant-wavelength data were adversely impacted if the magnetic structure was not included. A robust refinement weighting was found to be effective in reducing quantification errors using the constant-wavelength neutron data both where intensities from magnetic reflections were ignored and included. Results from the TOF data were very sensitive to inadequate modelling of the high- Q (low d-spacing) background using simple polynomials.« less

Species level identification of coagulase negative Staphylococcus spp. from buffalo using matrix-assisted laser desorption ionization-time of flight mass spectrometry and cydB real-time quantitative PCR.

PubMed

Pizauro, Lucas J L; de Almeida, Camila C; Soltes, Glenn A; Slavic, Durda; Rossi-Junior, Oswaldo D; de Ávila, Fernando A; Zafalon, Luiz F; MacInnes, Janet I

2017-05-01

Incorrect identification of Staphylococcus spp. can have serious clinical and zoonotic repercussions. Accordingly, the aim of this study was to determine if matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or cydB real- time quantitative PCR (qPCR) could be used to accurately identify coagulase negative Staphylococcus spp. (CoNS) obtained from buffalo milk and milking environment samples. Seventy-five of 84 CoNS isolates could be identified to the species level (score value >1.99) using MALDI-TOF MS. However, as determined by cytochrome d ubiquinol oxidase subunit II (cydB) qPCR and by 16S RNA and cydB gene sequencing, 10S. agnetis strains were wrongly identified as S. hyicus by MALDI-TOF MS. In addition, 9 isolates identified by MALDI-TOF only to the genus level (score values between 1.70 and 1.99) could be identified to species by cydB qPCR. Our findings suggest that MALDI-TOF MS is a reliable method for rapid identification of S. chromogenes and S. epidermidis (species of interest both in human and veterinary medicine) and may be able to correctly identify other Staphylococcus spp. However, at present not all Staphylococcus spp. found in buffalo milk can be accurately identified by MALDI-TOF MS and for these organisms, the cydB qPCR developed in the current study may provide a reliable alternative method for rapid identification of CoNS species. Copyright © 2017 Elsevier B.V. All rights reserved.

Modulation of cortical activity in 2D versus 3D virtual reality environments: an EEG study.

PubMed

Slobounov, Semyon M; Ray, William; Johnson, Brian; Slobounov, Elena; Newell, Karl M

2015-03-01

There is a growing empirical evidence that virtual reality (VR) is valuable for education, training, entertaining and medical rehabilitation due to its capacity to represent real-life events and situations. However, the neural mechanisms underlying behavioral confounds in VR environments are still poorly understood. In two experiments, we examined the effect of fully immersive 3D stereoscopic presentations and less immersive 2D VR environments on brain functions and behavioral outcomes. In Experiment 1 we examined behavioral and neural underpinnings of spatial navigation tasks using electroencephalography (EEG). In Experiment 2, we examined EEG correlates of postural stability and balance. Our major findings showed that fully immersive 3D VR induced a higher subjective sense of presence along with enhanced success rate of spatial navigation compared to 2D. In Experiment 1 power of frontal midline EEG (FM-theta) was significantly higher during the encoding phase of route presentation in the 3D VR. In Experiment 2, the 3D VR resulted in greater postural instability and modulation of EEG patterns as a function of 3D versus 2D environments. The findings support the inference that the fully immersive 3D enriched-environment requires allocation of more brain and sensory resources for cognitive/motor control during both tasks than 2D presentations. This is further evidence that 3D VR tasks using EEG may be a promising approach for performance enhancement and potential applications in clinical/rehabilitation settings. Copyright © 2014 Elsevier B.V. All rights reserved.

3D Indoor Positioning of UAVs with Spread Spectrum Ultrasound and Time-of-Flight Cameras

PubMed Central

Aguilera, Teodoro

2017-01-01

This work proposes the use of a hybrid acoustic and optical indoor positioning system for the accurate 3D positioning of Unmanned Aerial Vehicles (UAVs). The acoustic module of this system is based on a Time-Code Division Multiple Access (T-CDMA) scheme, where the sequential emission of five spread spectrum ultrasonic codes is performed to compute the horizontal vehicle position following a 2D multilateration procedure. The optical module is based on a Time-Of-Flight (TOF) camera that provides an initial estimation for the vehicle height. A recursive algorithm programmed on an external computer is then proposed to refine the estimated position. Experimental results show that the proposed system can increase the accuracy of a solely acoustic system by 70–80% in terms of positioning mean square error. PMID:29301211

MALDI-TOF Mass Spectrometry as a Useful Tool for Identification of Enterococcus spp. from Wild Birds and Differentiation of Closely Related Species.

PubMed

Stępień-Pyśniak, Dagmara; Hauschild, Tomasz; Różański, Paweł; Marek, Agnieszka

2017-06-28

The aim of this study was to explore the accuracy and feasibility of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying bacteria from environmental sources, as compared with rpoA gene sequencing, and to evaluate the occurrence of bacteria of the genus Enterococcus in wild birds. In addition, a phyloproteomic analysis of certain Enterococcus species with spectral relationships was performed. The enterococci were isolated from 25 species of wild birds in central Europe (Poland). Proteomic (MALDI-TOF MS) and genomic ( rpoA gene sequencing) methods were used to identify all the isolates. Using MALDI-TOF MS, all 54 (100%) isolates were identified as Enterococcus spp. Among these, 51 (94.4%) isolates were identified to the species level (log(score) > or =2.0), and three isolates (5.6%) were identified at a level of probable genus identification (log(score) 1.88-1.927). Phylogenetic analysis based on rpoA sequences confirmed that all enterococci had been correctly identified. Enterococcus faecalis was the most prevalent enterococcal species (50%) and Enterococcus faecium (33.3%) the second most frequent species, followed by Enterococcus hirae (9.3%), Enterococcus durans (3.7%), and Enterococcus casseliflavus (3.7%). The phyloproteomic analysis of the spectral profiles of the isolates showed that MALDI-TOF MS is able to differentiate among similar species of the genus Enterococcus .

Quantitative and Visual Assessments toward Potential Sub-mSv or Ultrafast FDG PET Using High-Sensitivity TOF PET in PET/MRI.

PubMed

Behr, Spencer C; Bahroos, Emma; Hawkins, Randall A; Nardo, Lorenzo; Ravanfar, Vahid; Capbarat, Emily V; Seo, Youngho

2018-06-01

Newer high-performance time-of-flight (TOF) positron emission tomography (PET) systems have the capability to preserve diagnostic image quality with low count density, while maintaining a high raw photon detection sensitivity that would allow for a reduction in injected dose or rapid data acquisition. To assess this, we performed quantitative and visual assessments of the PET images acquired using a highly sensitive (23.3 cps/kBq) large field of view (25-cm axial) silicon photomultiplier (SiPM)-based TOF PET (400-ps timing resolution) integrated with 3 T-MRI in comparison to PET images acquired on non-TOF PET/x-ray computed tomography (CT) systems. Whole-body 2-deoxy-2-[ 18 F]fluoro-D-glucose ([ 18 F]FDG) PET/CT was acquired for 15 patients followed by whole body PET/magnetic resonance imaging (MRI) with an average injected dose of 325 ± 84 MBq. The PET list mode data from PET/MRI were reconstructed using full datasets (4 min/bed) and reduced datasets (2, 1, 0.5, and 0.25 min/bed). Qualitative assessment between PET/CT and PET/MR images were made. A Likert-type scale between 1 and 5, 1 for non-diagnostic, 3 equivalent to PET/CT, and 5 superior quality, was used. Maximum and mean standardized uptake values (SUV max and SUV mean ) of normal tissues and lesions detected were measured and compared. Mean visual assessment scores were 3.54 ± 0.32, 3.62 ± 0.38, and 3.69 ± 0.35 for the brain and 3.05 ± 0.49, 3.71 ± 0.45, and 4.14 ± 0.44 for the whole-body maximum intensity projections (MIPs) for 1, 2, and 4 min/bed PET/MR images, respectively. The SUV mean values for normal tissues were lower and statistically significant for images acquired at 4, 2, 1, 0.5, and 0.25 min/bed on the PET/MR, with values of - 18 ± 28 % (p < 0.001), - 16 ± 29 % (p = 0.001), - 16 ± 31 % (p = 0.002), - 14 ± 35 % (p < 0.001), and - 13 ± 34 % (p = 0.002), respectively. SUV max and SUV peak values of all lesions were higher and statistically significant (p < 0.05) for 4, 2, 1, 0.50, and 0.25 min/bed PET/MR datasets. High-sensitivity TOF PET showed comparable but still better visual image quality even at a much reduced activity in comparison to lower-sensitivity non-TOF PET. Our data translates to a seven times reduction in either injection dose for the same time or total scan time for the same injected dose. This "ultra-sensitivity" PET system provides a path to clinically acceptable extremely low-dose FDG PET studies (e.g., sub 1 mCi injection or sub-mSv effective dose) or PET studies as short as 1 min/bed (e.g., 6 min of total scan time) to cover whole body without compromising diagnostic performance.

A magnetic particle time-of-flight (MagPTOF) diagnostic for measurements of shock- and compression-bang time at the NIF (invited)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinderknecht, H. G., E-mail: hgr@mit.edu; Sio, H.; Frenje, J. A.

A magnetic particle time-of-flight (MagPTOF) diagnostic has been designed to measure shock- and compression-bang time using D{sup 3}He-fusion protons and DD-fusion neutrons, respectively, at the National Ignition Facility (NIF). This capability, in combination with shock-burn weighted areal density measurements, will significantly constrain the modeling of the implosion dynamics. This design is an upgrade to the existing particle time-of-flight (pTOF) diagnostic, which records bang times using DD or DT neutrons with an accuracy better than ±70 ps [H. G. Rinderknecht et al., Rev. Sci. Instrum. 83, 10D902 (2012)]. The inclusion of a deflecting magnet will increase D{sup 3}He-proton signal-to-background by amore » factor of 1000, allowing for the first time simultaneous measurements of shock- and compression-bang times in D{sup 3}He-filled surrogate implosions at the NIF.« less

Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vater, Joachim; Niu, Ben; Dietel, Kristin; Borriss, Rainer

2015-09-01

Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α- and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of bn- and yn-ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr4. More than 10 novel fusaricidins were characterized mass spectrometrically.

PTR-3-TOF a novel in-situ instrument for studying the lifecycle of reactive organic carbon in the atmosphere

NASA Astrophysics Data System (ADS)

Hansel, Armin; Breitenlechner, Martin; Fischer, Lukas; Hainer, Markus

2017-04-01

Existing proton transfer reaction time of flight (PTR-TOF) instruments are known to detect volatile organic compounds (VOCs) and could in principle also detect highly oxidized organic compounds such as low volatility organic compounds (LVOC) but PTR-TOF inlets were not optimized to avoid wall losses of such low volatility compounds. In addition PTR-TOF is not sensitive enough to quantify second order and even higher order oxidation products at atmospherically relevant concentrations. To solve this problem, as well as to enable bridging the gap in understanding how atmospherically relevant BVOC form SVOC, LVOC and even ELVOC, we developed the PTR3, a compact and field deployable ultrasensitive instrument based on chemical ionization mass spectrometry. Here we report first results from PTR-3-TOF measurements at Hyytiälä where we measured concentrations and fluxes of precursor gases (BVOC) and their oxidation products: semi and low volatile organic compounds. The recently developed PTR-3-TOF instrument uses a discharge ion source coupled to a contact free inlet system running at high sample flow rates through the novel reaction chamber at 80 mbar. The PTR-3 front part is coupled to TOFWERK's newest Long-TOF mass analyzer. The first prototype has sensitivities of up to 20.000 cps per ppb and a mass resolution of 8.000 m/Δm. The instrument has been successfully tested at CERN for the CLOUD campaign in 2015. During pure α-pinene ozonolysis experiments at low NOx conditions we observed in total several hundred peaks in the mass spectrum, including α-Pinene present in the ppb range, first and higher order oxidation products present in the ppt range and highly oxydized α-pinene monomers and dimers (e.g., C20H30O18H+; m/z = 559.1506 Th) in the low ppq range and even sub-ppq range. The advantage of this new technology based on positive ion chemistry is the capability to measure precursor gases as well as condensing- and even nucleating vapors.

A laser desorption ionization/matrix-assisted laser desorption ionization target system applicable for three distinct types of instruments (LinTOF/curved field RTOF, LinTOF/RTOF and QqRTOF) with different performance characteristics from three vendors.

PubMed

Rados, Edita; Pittenauer, Ernst; Frank, Johannes; Varmuza, Kurt; Allmaier, Günter

2018-04-30

We have developed a target system which enables the use of only one target (i.e. target preparation set) for three different laser desorption ionization (LDI)/matrix-assisted laser desorption ionization (MALDI) mass spectrometric instruments. The focus was on analysing small biomolecules with LDI for future use of the system for the study of meteorite samples (carbonaceous chondrites) using devices with different mass spectrometric performance characteristics. Three compounds were selected due to their potential presence in meteoritic chondrites: tryptophan, 2-deoxy-d-ribose and triphenylene. They were prepared (with and without MALDI matrix, i.e. MALDI and LDI) and analysed with three different mass spectrometers (LinTOF/curved field RTOF, LinTOF/RTOF and QqRTOF). The ion sources of two of the instruments were run at high vacuum, and one at intermediate pressure. Two devices used a laser wavelength of 355 nm and one a wavelength of 337 nm. The developed target system operated smoothly with all devices. Tryptophan, 2-deoxy-d-ribose and triphenylene showed similar desorption/ionization behaviour for all instruments using the LDI mode. Interestingly, protonated tryptophan could be observed only with the LinTOF/curved field RTOF device in LDI and MALDI mode, while sodiated molecules were observed with all three instruments (in both ion modes). Deprotonated tryptophan was almost completely obscured by matrix ions in the MALDI mode whereas LDI yielded abundant deprotonated molecules. The presented target system allowed successful analyses of the three compounds using instruments from different vendors with only one preparation showing different analyser performance characteristics. The elemental composition with the QqRTOF analyser and the high-energy 20 keV collision-induced dissociation fragmentation will be important in identifying unknown compounds in chondrites. © 2018 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Whole lung morphometry with 3D multiple b-value hyperpolarized gas MRI and compressed sensing.

PubMed

Chan, Ho-Fung; Stewart, Neil J; Parra-Robles, Juan; Collier, Guilhem J; Wild, Jim M

2017-05-01

To demonstrate three-dimensional (3D) multiple b-value diffusion-weighted (DW) MRI of hyperpolarized 3 He gas for whole lung morphometry with compressed sensing (CS). A fully-sampled, two b-value, 3D hyperpolarized 3 He DW-MRI dataset was acquired from the lungs of a healthy volunteer and retrospectively undersampled in the k y and k z phase-encoding directions for CS simulations. Optimal k-space undersampling patterns were determined by minimizing the mean absolute error between reconstructed and fully-sampled 3 He apparent diffusion coefficient (ADC) maps. Prospective three-fold, undersampled, 3D multiple b-value 3 He DW-MRI datasets were acquired from five healthy volunteers and one chronic obstructive pulmonary disease (COPD) patient, and the mean values of maps of ADC and mean alveolar dimension (Lm D ) were validated against two-dimensional (2D) and 3D fully-sampled 3 He DW-MRI experiments. Reconstructed undersampled datasets showed no visual artifacts and good preservation of the main image features and quantitative information. A good agreement between fully-sampled and prospective undersampled datasets was found, with a mean difference of +3.4% and +5.1% observed in mean global ADC and Lm D values, respectively. These differences were within the standard deviation range and consistent with values reported from healthy and COPD lungs. Accelerated CS acquisition has facilitated 3D multiple b-value 3 He DW-MRI scans in a single breath-hold, enabling whole lung morphometry mapping. Magn Reson Med 77:1916-1925, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Radioembolization and the Dynamic Role of 90Y PET/CT

PubMed Central

Pasciak, Alexander S.; Bourgeois, Austin C.; McKinney, J. Mark; Chang, Ted T.; Osborne, Dustin R.; Acuff, Shelley N.; Bradley, Yong C.

2014-01-01

Before the advent of tomographic imaging, it was postulated that decay of 90 Y to the 0+ excited state of 90Zr may result in emission of a positron–electron pair. While the branching ratio for pair-production is small (~32 × 10−6), PET has been successfully used to image 90 Y in numerous recent patients and phantom studies. 90 Y PET imaging has been performed on a variety of PET/CT systems, with and without time-of-flight (TOF) and/or resolution recovery capabilities as well as on both bismuth-germanate and lutetium yttrium orthosilicate (LYSO)-based scanners. On all systems, resolution and contrast superior to bremsstrahlung SPECT has been reported. The intrinsic radioactivity present in LYSO-based PET scanners is a potential limitation associated with accurate quantification of 90 Y. However, intrinsic radioactivity has been shown to have a negligible effect at the high activity concentrations common in 90 Y radioembolization. Accurate quantification is possible on a variety of PET scanner models, with or without TOF, although TOF improves accuracy at lower activity concentrations. Quantitative 90 Y PET images can be transformed into 3-dimensional (3D) maps of absorbed dose based on the premise that the 90 Y activity distribution does not change after infusion. This transformation has been accomplished in several ways, although the most common is with the use of 3D dose-point-kernel convolution. From a clinical standpoint, 90 Y PET provides a superior post-infusion evaluation of treatment technical success owing to its improved resolution. Absorbed dose maps generated from quantitative PET data can be used to predict treatment efficacy and manage patient follow-up. For patients who receive multiple treatments, this information can also be used to provide patient-specific treatment-planning for successive therapies, potentially improving response. The broad utilization of 90 Y PET has the potential to provide a wealth of dose–response information, which may lead to development of improved radioembolization treatment-planning models in the future. PMID:24579065

Detailed two-dimensional gel proteomic mapping of the feces of the house dust mite Dermatophagoides pteronyssinus and comparison with D. farinae: Reduced trypsin protease content in D. pteronyssinus and different isoforms.

PubMed

Erban, Tomas; Harant, Karel; Hubert, Jan

2017-06-06

Major domestic mite allergens are present in feces. We present a detailed 2D-E-MS/MS proteomic analysis of the Dermatophagoides pteronyssinus feces. Precise cultivation yielded a pure fecal extract. We detected differences in fecal allergens/digestive enzymes between D. pteronyssinus and D. farinae using 2D-E fingerprinting, including unique information on species-specific protease isoforms. Proteomic analysis was performed by 2D-E coupled with MALDI-TOF/TOF identification. The species-specific differences in the fecal extracts of the mites were attributed to trypsin-like proteases known as group 3 allergens. In D. farinae, Der f 3 exhibited high abundance with a pI similar (acidic) to that of the cysteine protease Der f 1 and the chymotrypsin protease Der f 6, whereas in D. pteronyssinus, Der p 3 was rarely detected and exhibited low abundance only at basic pI. Moreover, Der p 9 was detected at a pI of ~ 10, in contrast to Der p 1 and Der p 6, suggesting different compartmentalization in the body. Overall, in D. pteronyssinus feces, allergens of groups 1, 2, 6, and 15 were quantitatively similar to those of D. farinae with the exception of the group 3 and 9 allergens. This work provides novel insights into mite-defecated proteins/digestive enzymes, which are important allergens. Millions of people are affected by allergy and asthma, and their number is growing. In homes, the major triggers of allergy and asthma are the house dust mites Dermatophagoides farinae and D. pteronyssinus, and a clear understanding of the development of diseases caused by these mites is needed. The major sources of mite allergens are their feces, which are deposited in the environment and are easily inhaled as part of aeroplankton. However, descriptions of and comparisons between the major fecal allergens of these two mites are lacking. This study shows that similar group 1 (cysteine protease), 2 (NPC2 family), 6 (chymotrypsin) and 15 (chitinase-like) allergens are present in the feces of these two mite species, as determined by 2D-E mapping, whereas group 3 (trypsin) and 9 (collagenolytic protease) allergens in the feces of the two species are different. The results provide unique MS/MS mapped fingerprints of mite species-specific isoforms in feces. The presence of ubiquitin in mite feces suggests that these proteins participate in the post-translational modification of fecal proteins. The findings are essential for understanding differences between D. farinae and D. pteronyssinus with respect to immunoreactivity, protease activation mechanisms, association with microbes, and food utilization. Copyright © 2017 Elsevier B.V. All rights reserved.

First in situ TOF-PET study using digital photon counters for proton range verification.

PubMed

Cambraia Lopes, P; Bauer, J; Salomon, A; Rinaldi, I; Tabacchini, V; Tessonnier, T; Crespo, P; Parodi, K; Schaart, D R

2016-08-21

Positron emission tomography (PET) is the imaging modality most extensively tested for treatment monitoring in particle therapy. Optimal use of PET in proton therapy requires in situ acquisition of the relatively strong (15)O signal due to its relatively short half-life (~2 min) and high oxygen content in biological tissues, enabling shorter scans that are less sensitive to biological washout. This paper presents the first performance tests of a scaled-down in situ time-of-flight (TOF) PET system based on digital photon counters (DPCs) coupled to Cerium-doped Lutetium Yttrium Silicate (LYSO:Ce) crystals, providing quantitative results representative of a dual-head tomograph that complies with spatial constraints typically encountered in clinical practice (2  ×  50°, of 360°, transaxial angular acceptance). The proton-induced activity inside polymethylmethacrylate (PMMA) and polyethylene (PE) phantoms was acquired within beam pauses (in-beam) and immediately after irradiation by an actively-delivered synchrotron pencil-beam, with clinically relevant 125.67 MeV/u, 4.6  ×  10(8) protons s(-1), and 10(10) total protons. 3D activity maps reconstructed with and without TOF information are compared to FLUKA simulations, demonstrating the benefit of TOF-PET to reduce limited-angle artefacts using a 382 ps full width at half maximum coincidence resolving time. The time-dependent contributions from different radionuclides to the total count-rate are investigated. We furthermore study the impact of the acquisition time window on the laterally integrated activity depth-profiles, with emphasis on 2 min acquisitions starting at different time points. The results depend on phantom composition and reflect the differences in relative contributions from the radionuclides originating from carbon and oxygen. We observe very good agreement between the shapes of the simulated and measured activity depth-profiles for post-beam protocols. However, our results also suggest that available experimental cross sections underestimate the production of (10)C for in-beam acquisitions, which in PE results in an overestimation of the predicted activity range by 1.4 mm. The uncertainty in the activity range measured in PMMA using the DPC-based TOF-PET prototype setup equals 0.2 mm-0.3 mm.

First in situ TOF-PET study using digital photon counters for proton range verification

NASA Astrophysics Data System (ADS)

Cambraia Lopes, P.; Bauer, J.; Salomon, A.; Rinaldi, I.; Tabacchini, V.; Tessonnier, T.; Crespo, P.; Parodi, K.; Schaart, D. R.

2016-08-01

Positron emission tomography (PET) is the imaging modality most extensively tested for treatment monitoring in particle therapy. Optimal use of PET in proton therapy requires in situ acquisition of the relatively strong 15O signal due to its relatively short half-life (~2 min) and high oxygen content in biological tissues, enabling shorter scans that are less sensitive to biological washout. This paper presents the first performance tests of a scaled-down in situ time-of-flight (TOF) PET system based on digital photon counters (DPCs) coupled to Cerium-doped Lutetium Yttrium Silicate (LYSO:Ce) crystals, providing quantitative results representative of a dual-head tomograph that complies with spatial constraints typically encountered in clinical practice (2  ×  50°, of 360°, transaxial angular acceptance). The proton-induced activity inside polymethylmethacrylate (PMMA) and polyethylene (PE) phantoms was acquired within beam pauses (in-beam) and immediately after irradiation by an actively-delivered synchrotron pencil-beam, with clinically relevant 125.67 MeV/u, 4.6  ×  108 protons s-1, and 1010 total protons. 3D activity maps reconstructed with and without TOF information are compared to FLUKA simulations, demonstrating the benefit of TOF-PET to reduce limited-angle artefacts using a 382 ps full width at half maximum coincidence resolving time. The time-dependent contributions from different radionuclides to the total count-rate are investigated. We furthermore study the impact of the acquisition time window on the laterally integrated activity depth-profiles, with emphasis on 2 min acquisitions starting at different time points. The results depend on phantom composition and reflect the differences in relative contributions from the radionuclides originating from carbon and oxygen. We observe very good agreement between the shapes of the simulated and measured activity depth-profiles for post-beam protocols. However, our results also suggest that available experimental cross sections underestimate the production of 10C for in-beam acquisitions, which in PE results in an overestimation of the predicted activity range by 1.4 mm. The uncertainty in the activity range measured in PMMA using the DPC-based TOF-PET prototype setup equals 0.2 mm-0.3 mm.

Structure of a Rhamnogalacturonan Fragment from Apple Pectin: Implications for Pectin Architecture

DOE PAGES

Wu, Xiangmei; Mort, Andrew

2014-01-01

A comore » mmercial apple pectin was sequentially digested with the cloned enzymes endopolygalacturonase, galactanase, arabinofuranosidase, xylogalacturonase, and rhamnogalacturonan hydrolase. The rhamnogalacturonan hydrolase-generated oligosaccharides were separated by ultrafiltration, anion exchange, and size-exclusion chromatography. Fractions from the ion exchange chromatography were pooled, lyophilized, and screened by MALDI-TOF MS. An oligosaccharide (RGP14P3) was identified and its structure, α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A, determined by 1D and 2D NMR spectrometry. This oligosaccharide probably represents a direct connection between homogalacturonan and rhamnogalacturonan in pectin. Alternatively, it could indicate that the nonreducing end of rhamnogalacturonan starts with a galacturonic acid residue.« less

Differences among the cell wall galactomannans from Aspergillus wentii and Chaetosartorya chrysella and that of Aspergillus fumigatus.

PubMed

Gómez-Miranda, Begoña; Prieto, Alicia; Leal, Juan Antonio; Ahrazem, Oussama; Jiménez-Barbero, Jesús; Bernabé, Manuel

2004-01-01

The alkali extractable and water-soluble cell wall polysaccharides F1SS from Aspergillus wentii and Chaetosartorya chrysella have been studied by methylation analysis, 1D- and 2D-NMR, and MALDI-TOF analysis. Their structures are almost identical, corresponding to the following repeating unit: [--> 3)-beta-D-Gal f -(1 --> 5)-beta-D-Gal f-(1 -->]n --> mannan core. The structure of this galactofuranose side chain differs from that found in the pathogenic fungus Aspergillus fumigatus, in other Aspergillii and members of Trichocomaceae: [--> 5)-beta-D-Gal f-(1 -->]n --> mannan core. The mannan cores have also been investigated, and are constituted by a (1 --> 6)-alpha-mannan backbone, substituted at positions 2 by chains from 1 to 7 residues of (1 --> 2) linked alpha-mannopyranoses. Copyright 2004 Kluwer Academic Publishers

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

EBM regeneration and changes in EBM component mRNA expression in stromal cells after corneal injury

PubMed Central

Santhanam, Abirami; Marino, Gustavo K.; Torricelli, Andre A. M.

2017-01-01

Purpose To investigate the production of the epithelial basement membrane (EBM) component mRNAs at time points before lamina lucida and lamina densa regeneration in anterior stromal cells after corneal injury that would heal with and without fibrosis. Methods Rabbit corneas were removed from 2 to 19 days after −4.5D or −9.0D photorefractive keratectomy (PRK) with the VISX S4 IR laser. Corneas were evaluated with transmission electron microscopy (TEM) for full regeneration of the lamina lucida and the lamina densa. Laser capture microdissection (LCM) based quantitative real-time (RT)–PCR was used to quantitate the expression of mRNAs for laminin α-3 (LAMA3), perlecan, nidogen-1, and nidogen-2 in the anterior stroma. Results After −4.5D PRK, EBM was found to be fully regenerated at 8 to 10 days after surgery. At 4 days after PRK, the nidogen-2 and LAMA3 mRNAs levels were detected at statistically significantly lower levels in the anterior stroma of the −9.0D PRK corneas (where the EBM would not fully regenerate) compared to the −4.5D PRK corneas (where the EBM was destined to fully regenerate). At 7 days after PRK, nidogen-2 and LAMA3 mRNAs continued to be statistically significantly lower in the anterior stroma of the −9.0D PRK corneas compared to their expression in the anterior stroma of the −4.5D PRK corneas. Conclusions Key EBM components LAMA3 and nidogen-2 mRNAs are expressed at higher levels in the anterior stroma during EBM regeneration in the −4.5D PRK corneas where the EBM is destined to fully regenerate and no haze developed compared to the −9.0D PRK corneas where the EBM will not fully regenerate and myofibroblast-related stromal fibrosis (haze) will develop. PMID:28275314

Metabolite profiling on apple volatile content based on solid phase microextraction and gas-chromatography time of flight mass spectrometry.

PubMed

Aprea, Eugenio; Gika, Helen; Carlin, Silvia; Theodoridis, Georgios; Vrhovsek, Urska; Mattivi, Fulvio

2011-07-15

A headspace SPME GC-TOF-MS method was developed for the acquisition of metabolite profiles of apple volatiles. As a first step, an experimental design was applied to find out the most appropriate conditions for the extraction of apple volatile compounds by SPME. The selected SPME method was applied in profiling of four different apple varieties by GC-EI-TOF-MS. Full scan GC-MS data were processed by MarkerLynx software for peak picking, normalisation, alignment and feature extraction. Advanced chemometric/statistical techniques (PCA and PLS-DA) were used to explore data and extract useful information. Characteristic markers of each variety were successively identified using the NIST library thus providing useful information for variety classification. The developed HS-SPME sampling method is fully automated and proved useful in obtaining the fingerprint of the volatile content of the fruit. The described analytical protocol can aid in further studies of the apple metabolome. Copyright © 2011 Elsevier B.V. All rights reserved.

Design and realization of retina-like three-dimensional imaging based on a MOEMS mirror

NASA Astrophysics Data System (ADS)

Cao, Jie; Hao, Qun; Xia, Wenze; Peng, Yuxin; Cheng, Yang; Mu, Jiaxing; Wang, Peng

2016-07-01

To balance conflicts for high-resolution, large-field-of-view and real-time imaging, a retina-like imaging method based on time-of flight (TOF) is proposed. Mathematical models of 3D imaging based on MOEMS are developed. Based on this method, we perform simulations of retina-like scanning properties, including compression of redundant information and rotation and scaling invariance. To validate the theory, we develop a prototype and conduct relevant experiments. The preliminary results agree well with the simulations.

Army Aviation Simulation Survey

DTIC Science & Technology

1992-07-01

B-53 4.2.1 Functions Performed by DE .......................................... B-53 4.2.2 Functions Performed by DAS...B-60 5-2. AFDD Employees in the Simulation Functional Area by Organizational Unit.. B-61 S5-3. RDEC DE /DAS Simulation Personnel Profile...tof Fi u e16st e R E’im ulation m d l n de i n t o s o c n ractivt rg vs. highse t prim e orit yc to B-46 I I I demands, there is an ongoing

Multisensory System for the Detection and Localization of Peripheral Subcutaneous Veins

PubMed Central

Fernández, Roemi; Armada, Manuel

2017-01-01

This paper proposes a multisensory system for the detection and localization of peripheral subcutaneous veins, as a first step for achieving automatic robotic insertion of catheters in the near future. The multisensory system is based on the combination of a SWIR (Short-Wave Infrared) camera, a TOF (Time-Of-Flight) camera and a NIR (Near Infrared) lighting source. The associated algorithm consists of two main parts: one devoted to the features extraction from the SWIR image, and another envisaged for the registration of the range data provided by the TOF camera, with the SWIR image and the results of the peripheral veins detection. In this way, the detected subcutaneous veins are mapped onto the 3D reconstructed surface, providing a full representation of the region of interest for the automatic catheter insertion. Several experimental tests were carried out in order to evaluate the capabilities of the presented approach. Preliminary results demonstrate the feasibility of the proposed design and highlight the potential benefits of the solution. PMID:28422075

Comparative Biochemical and Proteomic Analyses of Soybean Seed Cultivars Differing in Protein and Oil Content.

PubMed

Min, Chul Woo; Gupta, Ravi; Kim, So Wun; Lee, So Eui; Kim, Yong Chul; Bae, Dong Won; Han, Won Young; Lee, Byong Won; Ko, Jong Min; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

2015-08-19

This study develops differential protein profiles of soybean (Glycine max) seeds (cv. Saedanbaek and Daewon) varying in protein (47.9 and 39.2%) and oil (16.3 and 19.7%) content using protamine sulfate (PS) precipitation method coupled with a 2D gel electrophoresis (2DGE) approach. Of 71 detected differential spots between Daewon and Saedanbaek, 48 were successfully identified by MALDI-TOF/TOF. Gene ontology analysis revealed that up-regulated proteins in Saedanbaek were largely associated with nutrient reservoir activity (42.6%), which included mainly seed-storage proteins (SSPs; subunits of glycinin and β-conglycinin). Similar results were also obtained in two cultivars of wild soybean (G. soja cv. WS22 and WS15) differing in protein content. Western blots confirmed higher accumulation of SSPs in protein-rich Saedanbaek. Findings presented and discussed in this study highlight a possible involvement of the urea cycle for increased accumulation of SSPs and hence the higher protein content in soybean seeds.

Fluxes of isoprene and monoterpenes emitted by Tapajos National Forest, eastern central Amazonian rainforest, Santarem-PA, Brazil

NASA Astrophysics Data System (ADS)

Alves, E. G.; Batalha, S. S. A.; Park, J. H.; Seco, R.; Tota, J.; Santana, R. A. S. D.; Guenther, A. B.; Kim, S.; Smith, J. N.; Souza, R. A. F. D.

2014-12-01

Biogenic Volatile Organic Compounds (BVOCs) play an important role in atmospheric chemistry and biogeochemical cycles. It is known that tropical forests are the biggest source of the dominant BVOCs (i.e. isoprene and monoterpenes) emitted to the atmosphere. Nevertheless, Amazonian rainforest, the world's largest tropical rainforest, has been poorly explored for isoprene and monoterpene emissions. Recently (June and July 2014), we deployed a PTR-TOF-MS (Proton Transfer Reaction - Time of Flight - Mass Spectrometer) to quantify isoprene and monoterpene emissions using the eddy covariance flux method at the FLONA Tapajos (Floresta Nacional do Tapajos; Tapajos National Forest) in the eastern central Amazon rainforest, Santarem-PA, Brazil. The sample inlet and a 3D-sonic anemometer were located above the forest canopy (~65m), and the air was sampled through a long Teflon tube (100m) with high flow rate (40L/min) to the PTR-TOF-MS. From preliminary results for the first 3 days, concentrations and fluxes of m/z 69 (isoprene; C5H8-H+) and m/z 137 (total monoterpenes; C10H16-H+) showed a clear circadian cycle (high during daytime and low at nighttime), suggesting the emissions of these compounds are light and temperature dependent. Our study provides the first PTR-TOF-MS flux observations of isoprene and total monoterpenes at the Flona Tapajos. Moreover, since there are variations on the emissions, when comparing different environments of the huge Amazon basin, these results from eastern central Amazonia will contribute to improving regional and global BVOC emission model estimates.

Performance of the Tachyon Time-of-Flight PET Camera

NASA Astrophysics Data System (ADS)

Peng, Q.; Choong, W.-S.; Vu, C.; Huber, J. S.; Janecek, M.; Wilson, D.; Huesman, R. H.; Qi, Jinyi; Zhou, Jian; Moses, W. W.

2015-02-01

We have constructed and characterized a time-of-flight Positron Emission Tomography (TOF PET) camera called the Tachyon. The Tachyon is a single-ring Lutetium Oxyorthosilicate (LSO) based camera designed to obtain significantly better timing resolution than the 550 ps found in present commercial TOF cameras, in order to quantify the benefit of improved TOF resolution for clinically relevant tasks. The Tachyon's detector module is optimized for timing by coupling the 6.15 ×25 mm2 side of 6.15 ×6.15 ×25 mm3 LSO scintillator crystals onto a 1-inch diameter Hamamatsu R-9800 PMT with a super-bialkali photocathode. We characterized the camera according to the NEMA NU 2-2012 standard, measuring the energy resolution, timing resolution, spatial resolution, noise equivalent count rates and sensitivity. The Tachyon achieved a coincidence timing resolution of 314 ps +/- 20 ps FWHM over all crystal-crystal combinations. Experiments were performed with the NEMA body phantom to assess the imaging performance improvement over non-TOF PET. The results show that at a matched contrast, incorporating 314 ps TOF reduces the standard deviation of the contrast by a factor of about 2.3.

Performance of the Tachyon Time-of-Flight PET Camera.

PubMed

Peng, Q; Choong, W-S; Vu, C; Huber, J S; Janecek, M; Wilson, D; Huesman, R H; Qi, Jinyi; Zhou, Jian; Moses, W W

2015-02-01

We have constructed and characterized a time-of-flight Positron Emission Tomography (TOF PET) camera called the Tachyon. The Tachyon is a single-ring Lutetium Oxyorthosilicate (LSO) based camera designed to obtain significantly better timing resolution than the ~ 550 ps found in present commercial TOF cameras, in order to quantify the benefit of improved TOF resolution for clinically relevant tasks. The Tachyon's detector module is optimized for timing by coupling the 6.15 × 25 mm 2 side of 6.15 × 6.15 × 25 mm 3 LSO scintillator crystals onto a 1-inch diameter Hamamatsu R-9800 PMT with a super-bialkali photocathode. We characterized the camera according to the NEMA NU 2-2012 standard, measuring the energy resolution, timing resolution, spatial resolution, noise equivalent count rates and sensitivity. The Tachyon achieved a coincidence timing resolution of 314 ps +/- ps FWHM over all crystal-crystal combinations. Experiments were performed with the NEMA body phantom to assess the imaging performance improvement over non-TOF PET. The results show that at a matched contrast, incorporating 314 ps TOF reduces the standard deviation of the contrast by a factor of about 2.3.

Performance of the Tachyon Time-of-Flight PET Camera

PubMed Central

Peng, Q.; Choong, W.-S.; Vu, C.; Huber, J. S.; Janecek, M.; Wilson, D.; Huesman, R. H.; Qi, Jinyi; Zhou, Jian; Moses, W. W.

2015-01-01

We have constructed and characterized a time-of-flight Positron Emission Tomography (TOF PET) camera called the Tachyon. The Tachyon is a single-ring Lutetium Oxyorthosilicate (LSO) based camera designed to obtain significantly better timing resolution than the ~ 550 ps found in present commercial TOF cameras, in order to quantify the benefit of improved TOF resolution for clinically relevant tasks. The Tachyon’s detector module is optimized for timing by coupling the 6.15 × 25 mm2 side of 6.15 × 6.15 × 25 mm3 LSO scintillator crystals onto a 1-inch diameter Hamamatsu R-9800 PMT with a super-bialkali photocathode. We characterized the camera according to the NEMA NU 2-2012 standard, measuring the energy resolution, timing resolution, spatial resolution, noise equivalent count rates and sensitivity. The Tachyon achieved a coincidence timing resolution of 314 ps +/− ps FWHM over all crystal-crystal combinations. Experiments were performed with the NEMA body phantom to assess the imaging performance improvement over non-TOF PET. The results show that at a matched contrast, incorporating 314 ps TOF reduces the standard deviation of the contrast by a factor of about 2.3. PMID:26594057

Performance of the Tachyon Time-of-Flight PET Camera

DOE PAGES

Peng, Q.; Choong, W. -S.; Vu, C.; ...

2015-01-23

We have constructed and characterized a time-of-flight Positron Emission Tomography (TOF PET) camera called the Tachyon. The Tachyon is a single-ring Lutetium Oxyorthosilicate (LSO) based camera designed to obtain significantly better timing resolution than the ~ 550 ps found in present commercial TOF cameras, in order to quantify the benefit of improved TOF resolution for clinically relevant tasks. The Tachyon's detector module is optimized for timing by coupling the 6.15 ×25 mm 2 side of 6.15 ×6.15 ×25 mm 3 LSO scintillator crystals onto a 1-inch diameter Hamamatsu R-9800 PMT with a super-bialkali photocathode. We characterized the camera according tomore » the NEMA NU 2-2012 standard, measuring the energy resolution, timing resolution, spatial resolution, noise equivalent count rates and sensitivity. The Tachyon achieved a coincidence timing resolution of 314 ps +/- 20 ps FWHM over all crystal-crystal combinations. Experiments were performed with the NEMA body phantom to assess the imaging performance improvement over non-TOF PET. We find that the results show that at a matched contrast, incorporating 314 ps TOF reduces the standard deviation of the contrast by a factor of about 2.3.« less

Investigation of digital timing resolution and further improvement by using constant fraction signal time marker slope for fast scintillator detectors

NASA Astrophysics Data System (ADS)

Singh, Kundan; Siwal, Davinder

2018-04-01

A digital timing algorithm is explored for fast scintillator detectors, viz. LaBr3, BaF2, and BC501A. Signals were collected with CAEN 250 mega samples per second (MSPS) and 500 MSPS digitizers. The zero crossing time markers (TM) were obtained with a standard digital constant fraction timing (DCF) method. Accurate timing information is obtained using cubic spline interpolation of a DCF transient region sample points. To get the best time-of-flight (TOF) resolution, an optimization of DCF parameters is performed (delay and constant fraction) for each pair of detectors: (BaF2-LaBr3), (BaF2-BC501A), and (LaBr3-BC501A). In addition, the slope information of an interpolated DCF signal is extracted at TM position. This information gives a new insight to understand the broadening in TOF, obtained for a given detector pair. For a pair of signals having small relative slope and interpolation deviations at TM, leads to minimum time broadening. However, the tailing in TOF spectra is dictated by the interplay between the interpolation error and slope variations. Best TOF resolution achieved at the optimum DCF parameters, can be further improved by using slope parameter. Guided by the relative slope parameter, events selection can be imposed which leads to reduction in TOF broadening. While the method sets a trade-off between timing response and coincidence efficiency, it provides an improvement in TOF. With the proposed method, the improved TOF resolution (FWHM) for the aforementioned detector pairs are; 25% (0.69 ns), 40% (0.74 ns), 53% (0.6 ns) respectively, obtained with 250 MSPS, and corresponds to 12% (0.37 ns), 33% (0.72 ns), 35% (0.69 ns) respectively with 500 MSPS digitizers. For the same detector pair, event survival probabilities are; 57%, 58%, 51% respectively with 250 MSPS and becomes 63%, 57%, 68% using 500 MSPS digitizers.

The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members.

PubMed

Vetor, Ryan; Murray, Clinton K; Mende, Katrin; Melton-Kreft, Rachel; Akers, Kevin S; Wenke, Joseph; Spirk, Tracy; Guymon, Charles; Zera, Wendy; Beckius, Miriam L; Schnaubelt, Elizabeth R; Ehrlich, Garth; Vento, Todd J

2016-07-22

The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members. We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB. Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems. PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.

Total Laboratory Automation and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Improve Turnaround Times in the Clinical Microbiology Laboratory: a Retrospective Analysis.

PubMed

Theparee, Talent; Das, Sanchita; Thomson, Richard B

2018-01-01

Technological advances have changed the practice of clinical microbiology. We implemented Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and BD Kiestra total laboratory automation (TLA) 4 and 3 years ago, respectively. To assess the impact of these new technologies, we compared turnaround times (TATs) for positive and negative urine cultures before and after implementation. In comparison I, TATs for 61,157 urine cultures were extracted for two periods corresponding to pre-TLA and post-TLA, both using MALDI-TOF MS for organism identification. In comparison II, time to organism identification (ID) and antimicrobial susceptibility (AST) reports were calculated for 5,402 positive culture reports representing four different periods: (i) manual plating and conventional biochemical identification (CONV), (ii) manual plating and MALDI-TOF MS identification (MALDI), (iii) MALDI-TOF MS identification and early phase implementation of TLA (TLA1), and (iv) MALDI-TOF MS identification and late phase implementation of TLA (TLA2). By the comparison I results, median pre- and post-TLA TATs to organism IDs (18.5 to 16.9 h), AST results (41.8 to 40.8 h), and preliminary results for negative cultures (17.7 to 13.6 h), including interquartile ranges for all comparisons, were significantly decreased post-TLA ( P < 0.001). By the comparison II results, MALDI significantly improved TAT to organism ID compared to CONV (21.3 to 18 h). TLA further improved overall TAT to ID (18 to 16.5 h) and AST (42.3 to 40.7 h) results compared to MALDI ( P < 0.001). In summary, TLA significantly improved TAT to organism ID, AST report, and preliminary negative results. MALDI-TOF MS significantly improved TAT for organism ID. Use of MALDI-TOF MS and TLA individually and together results in significant decreases in microbiology report TATs. Copyright © 2017 Theparee et al.

Total Laboratory Automation and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Improve Turnaround Times in the Clinical Microbiology Laboratory: a Retrospective Analysis

PubMed Central

Theparee, Talent; Das, Sanchita

2017-01-01

ABSTRACT Technological advances have changed the practice of clinical microbiology. We implemented Bruker matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and BD Kiestra total laboratory automation (TLA) 4 and 3 years ago, respectively. To assess the impact of these new technologies, we compared turnaround times (TATs) for positive and negative urine cultures before and after implementation. In comparison I, TATs for 61,157 urine cultures were extracted for two periods corresponding to pre-TLA and post-TLA, both using MALDI-TOF MS for organism identification. In comparison II, time to organism identification (ID) and antimicrobial susceptibility (AST) reports were calculated for 5,402 positive culture reports representing four different periods: (i) manual plating and conventional biochemical identification (CONV), (ii) manual plating and MALDI-TOF MS identification (MALDI), (iii) MALDI-TOF MS identification and early phase implementation of TLA (TLA1), and (iv) MALDI-TOF MS identification and late phase implementation of TLA (TLA2). By the comparison I results, median pre- and post-TLA TATs to organism IDs (18.5 to 16.9 h), AST results (41.8 to 40.8 h), and preliminary results for negative cultures (17.7 to 13.6 h), including interquartile ranges for all comparisons, were significantly decreased post-TLA (P < 0.001). By the comparison II results, MALDI significantly improved TAT to organism ID compared to CONV (21.3 to 18 h). TLA further improved overall TAT to ID (18 to 16.5 h) and AST (42.3 to 40.7 h) results compared to MALDI (P < 0.001). In summary, TLA significantly improved TAT to organism ID, AST report, and preliminary negative results. MALDI-TOF MS significantly improved TAT for organism ID. Use of MALDI-TOF MS and TLA individually and together results in significant decreases in microbiology report TATs. PMID:29118171

Comparison of veterinary drug residue results in animal tissues by ultrahigh-performance liquid chromatography coupled to triple quadrupole or quadrupole-time-of-flight tandem mass spectrometry after different sample preparation methods, including use of a commercial lipid removal product.

PubMed

Anumol, Tarun; Lehotay, Steven J; Stevens, Joan; Zweigenbaum, Jerry

2017-04-01

Veterinary drug residues in animal-derived foods must be monitored to ensure food safety, verify proper veterinary practices, enforce legal limits in domestic and imported foods, and for other purposes. A common goal in drug residue analysis in foods is to achieve acceptable monitoring results for as many analytes as possible, with higher priority given to the drugs of most concern, in an efficient and robust manner. The U.S. Department of Agriculture has implemented a multiclass, multi-residue method based on sample preparation using dispersive solid phase extraction (d-SPE) for cleanup and ultrahigh-performance liquid chromatography-tandem quadrupole mass spectrometry (UHPLC-QQQ) for analysis of >120 drugs at regulatory levels of concern in animal tissues. Recently, a new cleanup product called "enhanced matrix removal for lipids" (EMR-L) was commercially introduced that used a unique chemical mechanism to remove lipids from extracts. Furthermore, high-resolution quadrupole-time-of-flight (Q/TOF) for (U)HPLC detection often yields higher selectivity than targeted QQQ analyzers while allowing retroactive processing of samples for other contaminants. In this study, the use of both d-SPE and EMR-L sample preparation and UHPLC-QQQ and UHPLC-Q/TOF analysis methods for shared spiked samples of bovine muscle, kidney, and liver was compared. The results showed that the EMR-L method provided cleaner extracts overall and improved results for several anthelmintics and tranquilizers compared to the d-SPE method, but the EMR-L method gave lower recoveries for certain β-lactam antibiotics. QQQ vs. Q/TOF detection showed similar mixed performance advantages depending on analytes and matrix interferences, with an advantage to Q/TOF for greater possible analytical scope and non-targeted data collection. Either combination of approaches may be used to meet monitoring purposes, with an edge in efficiency to d-SPE, but greater instrument robustness and less matrix effects when analyzing EMR-L extracts. Graphical abstract Comparison of cleanup methods in the analysis of veterinary drug residues in bovine tissues.

Effects of Different Maturation Systems on Bovine Oocyte Quality, Plasma Membrane Phospholipid Composition and Resistance to Vitrification and Warming.

PubMed

Sprícigo, José F W; Diógenes, Mateus N; Leme, Ligiane O; Guimarães, Ana L; Muterlle, Carolle V; Silva, Bianca Damiani Marques; Solà-Oriol, David; Pivato, Ivo; Silva, Luciano Paulino; Dode, Margot A N

2015-01-01

The objective of this study was to evaluate the effects of different maturation systems on oocyte resistance after vitrification and on the phospholipid profile of the oocyte plasma membrane (PM). Four different maturation systems were tested: 1) in vitro maturation using immature oocytes aspirated from slaughterhouse ovaries (CONT; n = 136); 2) in vitro maturation using immature oocytes obtained by ovum pick-up (OPU) from unstimulated heifers (IMA; n = 433); 3) in vitro maturation using immature oocytes obtained by OPU from stimulated heifers (FSH; n = 444); and 4) in vivo maturation using oocytes obtained from heifers stimulated 24 hours prior by an injection of GnRH (MII; n = 658). A sample of matured oocytes from each fresh group was analyzed by matrix associated laser desorption-ionization (MALDI-TOF) to determine their PM composition. Then, half of the matured oocytes from each group were vitrified/warmed (CONT VIT, IMA VIT, FSH VIT and MII VIT), while the other half were used as fresh controls. Afterwards, the eight groups underwent IVF and IVC, and blastocyst development was assessed at D2, D7 and D8. A chi-square test was used to compare embryo development between the groups. Corresponding phospholipid ion intensity was expressed in arbitrary units, and following principal components analyses (PCA) the data were distributed on a 3D graph. Oocytes obtained from superstimulated animals showed a greater rate of developmental (P<0.05) at D7 (MII = 62.4±17.5% and FSH = 58.8±16.1%) compared to those obtained from unstimulated animals (CONT = 37.9±8.5% and IMA = 50.6±14.4%). However, the maturation system did not affect the resistance of oocytes to vitrification because the blastocyst rate at D7 was similar (P>0.05) for all groups (CONT VIT = 2.8±3.5%, IMA VIT = 2.9±4.0%, FSH VIT = 4.3±7.2% and MII VIT = 3.6±7.2%). MALDI-TOF revealed that oocytes from all maturation groups had similar phospholipid contents, except for 760.6 ([PC (34:1) + H]+), which was more highly expressed in MII compared to FSH (P<0.05). The results suggest that although maturation systems improve embryonic development, they do not change the PM composition nor the resistance of bovine oocytes to vitrification.

Effects of Different Maturation Systems on Bovine Oocyte Quality, Plasma Membrane Phospholipid Composition and Resistance to Vitrification and Warming

PubMed Central

Sprícigo, José F. W.; Diógenes, Mateus N.; Leme, Ligiane O.; Guimarães, Ana L.; Muterlle, Carolle V.; Silva, Bianca Damiani Marques; Solà-Oriol, David; Pivato, Ivo; Silva, Luciano Paulino; Dode, Margot A. N.

2015-01-01

The objective of this study was to evaluate the effects of different maturation systems on oocyte resistance after vitrification and on the phospholipid profile of the oocyte plasma membrane (PM). Four different maturation systems were tested: 1) in vitro maturation using immature oocytes aspirated from slaughterhouse ovaries (CONT; n = 136); 2) in vitro maturation using immature oocytes obtained by ovum pick-up (OPU) from unstimulated heifers (IMA; n = 433); 3) in vitro maturation using immature oocytes obtained by OPU from stimulated heifers (FSH; n = 444); and 4) in vivo maturation using oocytes obtained from heifers stimulated 24 hours prior by an injection of GnRH (MII; n = 658). A sample of matured oocytes from each fresh group was analyzed by matrix associated laser desorption-ionization (MALDI-TOF) to determine their PM composition. Then, half of the matured oocytes from each group were vitrified/warmed (CONT VIT, IMA VIT, FSH VIT and MII VIT), while the other half were used as fresh controls. Afterwards, the eight groups underwent IVF and IVC, and blastocyst development was assessed at D2, D7 and D8. A chi-square test was used to compare embryo development between the groups. Corresponding phospholipid ion intensity was expressed in arbitrary units, and following principal components analyses (PCA) the data were distributed on a 3D graph. Oocytes obtained from superstimulated animals showed a greater rate of developmental (P<0.05) at D7 (MII = 62.4±17.5% and FSH = 58.8±16.1%) compared to those obtained from unstimulated animals (CONT = 37.9±8.5% and IMA = 50.6±14.4%). However, the maturation system did not affect the resistance of oocytes to vitrification because the blastocyst rate at D7 was similar (P>0.05) for all groups (CONT VIT = 2.8±3.5%, IMA VIT = 2.9±4.0%, FSH VIT = 4.3±7.2% and MII VIT = 3.6±7.2%). MALDI-TOF revealed that oocytes from all maturation groups had similar phospholipid contents, except for 760.6 ([PC (34:1) + H]+), which was more highly expressed in MII compared to FSH (P<0.05). The results suggest that although maturation systems improve embryonic development, they do not change the PM composition nor the resistance of bovine oocytes to vitrification. PMID:26107169

Comparison of PCR/electron spray ionization-time-of-flight-mass spectrometry versus traditional clinical microbiology for active surveillance of organisms contaminating high-use surfaces in a burn intensive care unit, an orthopedic ward and healthcare workers.

PubMed

Yun, Heather C; Kreft, Rachael E; Castillo, Mayra A; Ehrlich, Garth D; Guymon, Charles H; Crouch, Helen K; Chung, Kevin K; Wenke, Joseph C; Hsu, Joseph R; Spirk, Tracy L; Costerton, J William; Mende, Katrin; Murray, Clinton K

2012-10-10

Understanding nosocomial pathogen transmission is restricted by culture limitations. Novel platforms, such as PCR-based electron spray ionization-time-of-flight-mass spectrometry (ESI-TOF-MS), may be useful as investigational tools. Traditional clinical microbiology (TCM) and PCR/ESI-TOF-MS were used to recover and detect microorganisms from the hands and personal protective equipment of 10 burn intensive care unit (ICU) healthcare workers providing clinical care at a tertiary care military referral hospital. High-use environmental surfaces were assessed in 9 burn ICU and 10 orthopedic patient rooms. Clinical cultures during the study period were reviewed for pathogen comparison with investigational molecular diagnostic methods. From 158 samples, 142 organisms were identified by TCM and 718 by PCR/ESI-TOF-MS. The molecular diagnostic method detected more organisms (4.5 ± 2.1 vs. 0.9 ± 0.8, p < 0.01) from 99% vs. 67% of samples (p < 0.01). TCM detected S. aureus in 13 samples vs. 21 by PCR/ESI-TOF-MS. Gram-negative organisms were less commonly identified than gram-positive by both methods; especially by TCM. Among all detected bacterial species, similar percentages were typical nosocomial pathogens (18-19%) for TCM vs. PCR/ESI-TOF-MS. PCR/ESI-TOF-MS also detected mecA in 112 samples, vanA in 13, and KPC-3 in 2. MecA was associated (p < 0.01) with codetection of coagulase negative staphylococci but not S. aureus. No vanA was codetected with enterococci; one KPC-3 was detected without Klebsiella spp. In this pilot study, PCR/ESI-TOF-MS detected more organisms, especially gram-negatives, compared to TCM, but the current assay format is limited by the number of antibiotic resistance determinants it covers. Further large-scale assessments of PCR/ESI-TOF-MS for hospital surveillance are warranted.

Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm

PubMed Central

Huang, Bin; Zhang, Lei; Zhang, Weizheng; Liao, Kang; Zhang, Shihong; Zhang, Zhiquan; Ma, Xingyan; Chen, Jialong; Zhang, Xiuhong; Qu, Pinghua; Wu, Shangwei

2017-01-01

ABSTRACT Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allow prompt and specific treatment. We optimized specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile, and supernatant spotted onto the target plate were 15 ml, 3 μl, and 3 μl, respectively, yielding a LOD of 1.0 × 105 CFU/ml. Among a total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were, respectively, positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS alone and MALDI-TOF MS coupled with UA were 86.6% versus 93.4% (χ2 = 8.93; P < 0.01), 91.5% versus 96.3% (χ2 = 7.06; P < 0.01), 81.5% versus 96.4% (χ2 = 37.32; P < 0.01), and 94.1% versus 93.1% (χ2 = 0.40; P > 0.05), respectively. No significant performance differences were revealed among the three sites, while specificity and NPV of MALDI-TOF MS for males were significantly higher than those for females (specificity, 94.3% versus 77.3%, χ2 = 44.90, P < 0.01; NPV, 95.5% versus 86.1%, χ2 = 18.85, P < 0.01). Our results indicated that the optimization of specimen processing significantly enhanced analytical sensitivity and that the combination of UA and MALDI-TOF MS provided an accurate and rapid detection and identification of bacterial pathogens directly from urine. PMID:28249997

Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm.

PubMed

Huang, Bin; Zhang, Lei; Zhang, Weizheng; Liao, Kang; Zhang, Shihong; Zhang, Zhiquan; Ma, Xingyan; Chen, Jialong; Zhang, Xiuhong; Qu, Pinghua; Wu, Shangwei; Chen, Cha; Tang, Yi-Wei

2017-05-01

Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allow prompt and specific treatment. We optimized specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile, and supernatant spotted onto the target plate were 15 ml, 3 μl, and 3 μl, respectively, yielding a LOD of 1.0 × 10 5 CFU/ml. Among a total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were, respectively, positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS alone and MALDI-TOF MS coupled with UA were 86.6% versus 93.4% (χ 2 = 8.93; P < 0.01), 91.5% versus 96.3% (χ 2 = 7.06; P < 0.01), 81.5% versus 96.4% (χ 2 = 37.32; P < 0.01), and 94.1% versus 93.1% (χ 2 = 0.40; P > 0.05), respectively. No significant performance differences were revealed among the three sites, while specificity and NPV of MALDI-TOF MS for males were significantly higher than those for females (specificity, 94.3% versus 77.3%, χ 2 = 44.90, P < 0.01; NPV, 95.5% versus 86.1%, χ 2 = 18.85, P < 0.01). Our results indicated that the optimization of specimen processing significantly enhanced analytical sensitivity and that the combination of UA and MALDI-TOF MS provided an accurate and rapid detection and identification of bacterial pathogens directly from urine. Copyright © 2017 American Society for Microbiology.

Analysis of the endogenous peptide profile of milk: identification of 248 mainly casein-derived peptides.

PubMed

Baum, Florian; Fedorova, Maria; Ebner, Jennifer; Hoffmann, Ralf; Pischetsrieder, Monika

2013-12-06

Milk is an excellent source of bioactive peptides. However, the composition of the native milk peptidome has only been partially elucidated. The present study applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) directly or after prefractionation of the milk peptides by reverse-phase high-performance liquid chromatography (RP-HPLC) or OFFGEL fractionation for the comprehensive analysis of the peptide profile of raw milk. The peptide sequences were determined by MALDI-TOF/TOF or nano-ultra-performance liquid chromatography-nanoelectrospray ionization-LTQ-Orbitrap-MS. Direct MALDI-TOF-MS analysis led to the assignment of 57 peptides. Prefractionation by both complementary methods led to the assignment of another 191 peptides. Most peptides originate from α(S1)-casein, followed by β-casein, and α(S2)-casein. κ-Casein and whey proteins seem to play only a minor role as peptide precursors. The formation of many, but not all, peptides could be explained by the activity of the endogenous peptidases, plasmin or cathepsin D, B, and G. Database searches revealed the presence of 22 peptides with established physiological function, including those with angiotensin-converting-enzyme (ACE) inhibitory, immunomodulating, or antimicrobial activity.

A multiplexed TOF and DOI capable PET detector using a binary position sensitive network.

PubMed

Bieniosek, M F; Cates, J W; Levin, C S

2016-11-07

Time of flight (TOF) and depth of interaction (DOI) capabilities can significantly enhance the quality and uniformity of positron emission tomography (PET) images. Many proposed TOF/DOI PET detectors require complex readout systems using additional photosensors, active cooling, or waveform sampling. This work describes a high performance, low complexity, room temperature TOF/DOI PET module. The module uses multiplexed timing channels to significantly reduce the electronic readout complexity of the PET detector while maintaining excellent timing, energy, and position resolution. DOI was determined using a two layer light sharing scintillation crystal array with a novel binary position sensitive network. A 20 mm effective thickness LYSO crystal array with four 3 mm  ×  3 mm silicon photomultipliers (SiPM) read out by a single timing channel, one energy channel and two position channels achieved a full width half maximum (FWHM) coincidence time resolution of 180  ±  2 ps with 10 mm of DOI resolution and 11% energy resolution. With sixteen 3 mm  ×  3 mm SiPMs read out by a single timing channel, one energy channel and four position channels a coincidence time resolution 204  ±  1 ps was achieved with 10 mm of DOI resolution and 15% energy resolution. The methods presented here could significantly simplify the construction of high performance TOF/DOI PET detectors.

A high speed and high gain CMOS receiver chip for a pulsed time-of-flight laser rangefinder

NASA Astrophysics Data System (ADS)

Yu, Jin-jin; Deng, Ruo-han; Yuan, Hong-hui; Chen, Yong-ping

2011-06-01

An integrated receiver channel for a pulsed time-of-flight (TOF) laser rangefinder has been designed. Pulsed TOF laser range finding devices using a laser diode transmitter can achieve millimeter-level distance measurement accuracy in a measurement range of several tens of meters to non-cooperative targets. The amplifier exploits the regulated cascade (RGC) configuration as the input-stage, thus achieving as large effective input trans-conductance as that of Si Bipolar or GaAs MESFET. The RGC input configuration isolates the input parasitic capacitance including photodiode capacitance from the bandwidth determination better than common-gate TIA. To enlarge the bandwidth, inductive peaking technology has been adopted. An active inductor (MOS-L) is used instead of spiral inductor in CMOS process. An R-2R resistor ladder is inserting between per-amplifier and post-amplifier as the variable attenuator for digital gain control purpose. The gain-bandwidth of a basic differential pair with resistive load is not large enough for broad band operation. A circuit solution to improve both gain and bandwidth of an amplifying stage is proposed. Traditional and modified Cherry-Hooper amplifiers are discussed and the cascading of several stages to constitute the post-amplifier is designed. The fully integrated one-chip solution is designed with Cadence IC design platform. The simulation result shows the bandwidth of the trans-impedance amplifier is 215MHz with the presence of a 2pF input capacitor and 5pF load capacitor. And the maximum trans-impedance gain is 136dB. The walk error is less than 1ns in 1:1000 dynamic range. The responsive time is less than 2.2ns.

The Role of Conventional and Right-Sided ECG Screening for Subcutaneous ICD in a Tetralogy of Fallot Population.

PubMed

Alonso, Pau; Osca, Joaquín; Cano, Oscar; Pimenta, Pedro; Andrés, Ana; Yagüe, Jaime; Millet, José; Rueda, Joaquín; Sancho-Tello, María José

2017-02-01

Information regarding suitability for subcutaneous implantable cardioverter-defibrillator (S-ICD) implant in tetralogy of Fallot (ToF) population is scarce and needs to be further explored. (1) to determine the proportion of patients with ToF eligible for S-ICD, (2) to identify the optimal sensing vector in ToF patients, (3) to test specifically the eligibility for S-ICD with right-sided screening, and (4) to compare with the proportion of eligible patients in a nonselected ICD population. We recruited 60 consecutive patients with ToF and 40 consecutive nonselected patients. Conventional electrocardiographic screening was performed as usual. Right-sided alternative screening was studied by positioning the left arm and right arm electrodes 1 cm right lateral to the xiphoid midline. The Boston Scientific electrocardiogram (ECG) screening tool was utilized. We found a higher proportion of patients with right-sided positive screening in comparison with standard screening (77 ± 0.4% vs. 67 ± 0.4%; P < 0.0001) and a trend to higher number of appropriate leads in right-sided screening (1.3 ± 1 vs. 1.1 ± 1 ms; P = 0.07). Patients who failed the screening had a longer QRS duration and longer QT interval. Standard and right-sided screening showed a higher percent of positive patients in the control group compared to ToF patients (P < 0.001). Right-sided screening was associated with a significant 10% increase in S-ICD eligibility in ToF patients. When comparing with an acquired cardiomyopathies group, ToF showed a lower eligibility for S-ICD. The most appropriate ECG vector was the alternate vector in contrast to what is observed in the general population. © 2017 Wiley Periodicals, Inc.

Tetralogy of Fallot and aortic root dilation: a long-term outlook.

PubMed

Nagy, Christian D; Alejo, Diane E; Corretti, Mary C; Ravekes, William J; Crosson, Jane E; Spevak, Philip J; Ringel, Richard; Carson, Kathryn A; Khalil, Sara; Dietz, Harry C; Cameron, Duke E; Vricella, Luca A; Traill, Thomas A; Holmes, Kathryn W

2013-04-01

Dilation of the sinus of Valsalva (SoV) has been increasingly observed after repaired tetralogy of Fallot (TOF). We estimate the prevalence of SoV dilation in adults with repaired TOF and analyze possible factors related to aortic disease. Adults with TOF [n = 109, median age 33.2 years (range 18.1 to 69.5)] evaluated at Johns Hopkins Hospital from 2001 to 2009 were reviewed in an observational retrospective cohort study. Median follow-up was 27.3 (range 0.1-48.8) years. SoV dilation was defined as >95 % confidence interval adjusted for age and body surface area (z-score > 2). The prevalence of SoV dilation was 51 % compared with that of a normal population with a mean z-score of 2.03. Maximal aortic diameters were ≥ 4 cm in 39 % (42 of 109), ≥ 4.5 cm in 21 % (23 of 109), ≥ 5 cm in 8 % (9 of 109), and ≥ 5.5 cm in 2 % (2 of 109). There was no aortic dissection or death due contributable to aortic disease. Aortic valve replacement was performed in 1.8 % and aortic root or ascending aorta (AA) replacement surgery in 2.8 % of patients. By multivariate logistic regression analysis, aortic regurgitation (AR) [odds ratio (OR) = 3.09, p = 0.005], residual ventricular septal defect (VSD) (OR = 4.14, p < 0.02), and TOF with pulmonary atresia (TOF/PA) (OR = 6.75, p = 0.03) were associated with increased odds of dilated aortic root. SoV dilation after TOF repair is common and persists with aging. AR, residual VSD, and TOF/PA are associated with increased odds of dilation. AA evaluation beyond the SoV is important. Indexed values are imperative to avoid bias on the basis of age and body surface area.

The Effect of Susceptibility Artifacts Related to Metallic Implants on Adjacent-Lesion Assessment in Simultaneous TOF PET/MR.

PubMed

Svirydenka, Hanna; Delso, Gaspar; De Galiza Barbosa, Felipe; Huellner, Martin; Davison, Helen; Fanti, Stefano; Veit-Haibach, Patrick; Ter Voert, Edwin E G W

2017-07-01

Metalic implants may affect attenuation correction (AC) in PET/MR imaging. The purpose of this study was to evaluate the effect of susceptibility artifacts related to metallic implants on adjacent metabolically active lesions in clinical simultaneous PET/MR scanning for both time-of-flight (TOF) and non-TOF reconstructed PET images. Methods: We included 27 patients without implants but with confirmed 18 F-FDG-avid lesions adjacent to common implant locations. In all patients, a clinically indicated whole-body 18 F-FDG PET/MR scan was acquired. Baseline non-TOF and TOF PET images were reconstructed. Reconstruction was repeated after the introduction of artificial signal voids in the AC map to simulate metallic implants in standard anatomic areas. All reconstructed images were qualitatively and quantitatively assessed and compared with the baseline images. Results: In total, 51 lesions were assessed. In 40 and 50 of these cases (non-TOF and TOF, respectively), the detectability of the lesions did not change; in 9 and 1 cases, the detectability changed; and in 2 non-TOF cases, the lesions were no longer visible after the introduction of metallic artifacts. The inclusion of TOF information significantly reduced artifacts due to simulated implants in the femoral head, sternum, and spine ( P = 0.01, 0.01, and 0.03, respectively). It also improved image quality in these locations ( P = 0.02, 0.01, and 0.01, respectively). The mean percentage error was -3.5% for TOF and -4.8% for non-TOF reconstructions, meaning that the inclusion of TOF information reduced the percentage error in SUV max by 28.5% ( P < 0.01). Conclusion: Qualitatively, there was a significant reduction of artifacts in the femoral head, sternum, and spine. There was also a significant qualitative improvement in image quality in these locations. Furthermore, our study indicated that simulated susceptibility artifacts related to metallic implants have a significant effect on small, moderately 18 F-FDG-avid lesions near the implant site that possibly may go unnoticed without TOF information. On larger, highly 18 F-FDG-avid lesions, the metallic implants had only a limited effect. The largest significant quantitative difference was found in artifacts of the sternum. There was only a weak inverse correlation between lesions affected by artifacts and distance from the implant. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Genetic variations of VEGF gene were associated with tetralogy of fallot risk in a Chinese Han population.

PubMed

Yan, Liru; Ge, Quanzhi; Xi, Chunyan; Zhang, Xuna; Guo, Yujie

2015-05-01

Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. In this study, we aimed at investigating the associations between genetic variations of vascular endothelial growth factor (VEGF) gene and the risk of TOF in a Chinese Han population. Our findings may contribute to a deeper understanding of TOF pathogenesis and better diagnostic and therapeutic suggestions. A total of 165 TOF patients and 240 controls from a Chinese Han population in Shenyang and Harbin were recruited in the current study. Nine single-nucleotide polymorphisms (SNPs) (-2578C/A, -460T/C, -1154G/A, -634G/C, 534C/T, +398G/A, +963C/T, 752C/T, 913G/A) were genotyped by the MALDI-TOF MassARRAY system. Individual SNPs as well as their haplotypes were analyzed for their associations with TOF risk, using odds ratios and the 95% confidence interval under codominant and dominant models. In the single SNP analyses, the mutant homozygous genotypes of -2578C/A (rs699947) and +963C/T (rs3025039) were related with an increased risk of TOF. In addition, carriers with the mutant A allele of -1154G/A (rs1570360) were supposed to have a significantly elevated TOF risk. Similarly, compared with the wild homozygote GG carriers, the GC carrier of -634G/C (rs2010963) revealed a significant relationship with susceptibility of TOF, but not for the mutant homozygote CC carriers. However, no significant association was found for the other five SNPs. Meanwhile, haplotype analysis revealed that CCA and ATA in block 1 (-2578C/A, -460T/C, and -1154G/A) and TTG and TCA in block 3 (+963C/T, 752C/T, and 913G/A) were significantly related with an increased TOF risk compared with the most common haplotypes. In summary, our results suggested that VEGF variants (-2578C/A, -1154G/A, -634G/C, +963G/A) were involved in the susceptibility of TOF. However, validation of our study needs further study in various ethnics to reveal the functional relationship between VEGF polymorphisms and TOF risk, which may contribute to diagnosis and therapy of TOF.

Synthesis, characterization and investigation of electrochemical and spectroelectrochemical properties of non-peripherally tetra-5-methyl-1,3,4-thiadiazole substituted copper(II) iron(II) and oxo-titanium (IV) phthalocyanines

NASA Astrophysics Data System (ADS)

Demirbaş, Ümit; Akyüz, Duygu; Akçay, Hakkı Türker; Barut, Burak; Koca, Atıf; Kantekin, Halit

2017-09-01

In this study novel substituted phthalonitrile (3) and non-peripherally tetra 5-Methyl-1,3,4-thiadiazole substituted copper(II) (4), iron(II) (5) and oxo-titanium (IV) (6) phthalocyanines were synthesized. These novel compounds were fully characterized by FT-IR, 1H NMR, UV-vis and MALDI-TOF mass spectroscopic techniques. Voltammetric and in situ spectroelectrochemical measurements were performed for metallo-phthalocyanines (4-6). TiIVOPc and FeIIPc showed metal-based and ligand-based electron transfer reactions while CuIIPc shows only ligand-based electron transfer reaction. Voltammetric measurements indicated that the complexes have reversible, diffusion controlled and one-electron redox reactions. The assignments of the redox processes and color of the electrogenerated species of the complexes were determined with in-situ spectroelectrochemical and electrocolorimetric measurements. These measurements showed that the complexes can be used as the electrochromic materials for various display technologies.

High-throughput proteomic characterization of plasma rich in growth factors (PRGF-Endoret)-derived fibrin clot interactome.

PubMed

Anitua, Eduardo; Prado, Roberto; Azkargorta, Mikel; Rodriguez-Suárez, Eva; Iloro, Ibon; Casado-Vela, Juan; Elortza, Felix; Orive, Gorka

2015-11-01

Plasma rich in growth factors (PRGF®-Endoret®) is an autologous technology that contains a set of proteins specifically addressed to wound healing and tissue regeneration. The scaffold formed by using this technology is a clot mainly composed of fibrin protein, forming a three-dimensional (3D) macroscopic network. This biomaterial is easily obtained by biotechnological means from blood and can be used in a range of situations to help wound healing and tissue regeneration. Although the main constituent of this clot is the fibrin scaffold, little is known about other proteins interacting in this clot that may act as adjuvants in the healing process. The aim of this study was to characterize the proteins enclosed by PRGF-Endoret scaffold, using a double-proteomic approach that combines 1D-SDS-PAGE approach followed by LC-MS/MS, and 2-DE followed by MALDI-TOF/TOF. The results presented here provide a description of the catalogue of key proteins in close contact with the fibrin scaffold. The obtained lists of proteins were grouped into families and networks according to gene ontology. Taken together, an enrichment of both proteins and protein families specifically involved in tissue regeneration and wound healing has been found. Copyright © 2013 John Wiley & Sons, Ltd.

First characterization of a digital SiPM based time-of-flight PET detector with 1 mm spatial resolution

NASA Astrophysics Data System (ADS)

Seifert, Stefan; van der Lei, Gerben; van Dam, Herman T.; Schaart, Dennis R.

2013-05-01

Monolithic scintillator detectors can offer a combination of spatial resolution, energy resolution, timing performance, depth-of-interaction information, and detection efficiency that make this type of detector a promising candidate for application in clinical, time-of-flight (TOF) positron emission tomography (PET). In such detectors the scintillation light is distributed over a relatively large number of photosensor pixels and the light intensity per pixel can be relatively low. Therefore, monolithic scintillator detectors are expected to benefit from the low readout noise offered by a novel photosensor called the digital silicon photomultiplier (dSiPM). Here, we present a first experimental characterization of a TOF PET detector comprising a 24 × 24 × 10 mm3 LSO:Ce,0.2%Ca scintillator read out by a dSiPM array (DPC-6400-44-22) developed by Philips Digital Photon Counting. A spatial resolution of ˜1 mm full-width-at-half-maximum (FWHM) averaged over the entire crystal was obtained (varying from just below 1 mm FWHM in the detector center to ˜1.2 mm FWHM close to the edges). Furthermore, the bias in the position estimation at the crystal edges that is typically found in monolithic scintillators is well below 1 mm even in the corners of the crystal.

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories ▿

PubMed Central

van Veen, S. Q.; Claas, E. C. J.; Kuijper, Ed J.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory. PMID:20053859

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.

PubMed

van Veen, S Q; Claas, E C J; Kuijper, Ed J

2010-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

Dynamic of negative ions in potassium-D-ribose collisions.

PubMed

Almeida, D; Ferreira da Silva, F; García, G; Limão-Vieira, P

2013-09-21

We present negative ion formation from collisions of neutral potassium atoms with D-ribose (C5H10O5), the sugar unit in the DNA/RNA molecule. From the negative ion time-of-flight (TOF) mass spectra, OH(-) is the main fragment detected in the collision range 50-100 eV accounting on average for 50% of the total anion yield. Prominence is also given to the rich fragmentation pattern observed with special attention to O(-) (16 m/z) formation. These results are in sharp contrast to dissociative electron attachment experiments. The TOF mass spectra assignments show that these channels are also observed, albeit with a much lower relative intensity. Branching ratios of the most abundant fragment anions as a function of the collision energy are obtained, allowing to establish a rationale on the collision dynamics.

Associations between N-terminal pro-B-type natriuretic peptide and cardiac function in adults with corrected tetralogy of Fallot.

PubMed

Eindhoven, Jannet A; Menting, Myrthe E; van den Bosch, Annemien E; Cuypers, Judith A A E; Ruys, Titia P E; Witsenburg, Maarten; McGhie, Jackie S; Boersma, Eric; Roos-Hesselink, Jolien W

2014-07-01

Amino-terminal B-type natriuretic peptide (NT-proBNP) may detect early cardiac dysfunction in adults with tetralogy of Fallot (ToF) late after corrective surgery. We aimed to determine the value of NT-proBNP in adults with ToF and establish its relationship with echocardiography and exercise capacity. NT-proBNP measurement, electrocardiography and detailed 2D-echocardiography were performed on the same day in 177 consecutive adults with ToF (mean age 34.6 ± 11.8 years, 58% male, 89% NYHA I, 29.3 ± 8.5 years after surgical correction). Thirty-eight percent of the patients also underwent a cardiopulmonary-exercise test. Median NT-proBNP was 16 [IQR 6.7-33.6] pmol/L, and was elevated in 55%. NT-proBNP correlated with right ventricular (RV) dilatation (r = 0.271, p < 0.001) and RV systolic dysfunction (r = -0.195, p = 0.022), but more strongly with LV systolic dysfunction (r=-0.367, p<0.001), which was present in 69 patients (39%). Moderate or severe pulmonary regurgitation was not associated with higher NT-proBNP. Tricuspid and pulmonary regurgitation peak velocities correlated with NT-proBNP (r = 0.305, p < 0.001 and r = 0.186, p = 0.045, respectively). LV twist was measured with speckle-tracking echocardiography in 71 patients. An abnormal LV twist (20 patients, 28%) was associated with elevated NT-proBNP (p = 0.030). No relationship between NT-proBNP and exercise capacity was found. NT-proBNP levels are elevated in more than 50% of adults with corrected ToF, while they are in stable clinical condition. Higher NT-proBNP is most strongly associated with elevated pulmonary pressures, and with LV dysfunction rather than RV dysfunction. NT-proBNP has the potential to become routine examination in patients with ToF to monitor ventricular function and may be used for timely detection of clinical deterioration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Externally Calibrated Parallel Imaging for 3D Multispectral Imaging Near Metallic Implants Using Broadband Ultrashort Echo Time Imaging

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Reeder, Scott B.

2017-01-01

Purpose To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. Theory and Methods A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Results Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. Conclusion A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. PMID:27403613

Implications for Extraterrestrial Hydrocarbon Chemistry: Analysis of Ethylene (C2H4) and D4-Ethylene (C2D4) Ices Exposed to Ionizing Radiation via Combined Infrared Spectroscopy and Reflectron Time-of-flight Mass Spectrometry

NASA Astrophysics Data System (ADS)

Abplanalp, Matthew J.; Kaiser, Ralf I.

2017-02-01

The processing of the hydrocarbon ice, ethylene (C2H4/C2D4), via energetic electrons, thus simulating the processes in the track of galactic cosmic-ray particles, was carried out in an ultrahigh vacuum apparatus. The chemical evolution of the ices was monitored online and in situ utilizing Fourier transform infrared spectroscopy (FTIR) and during temperature programmed desorption, via a quadrupole mass spectrometer utilizing electron impact ionization (EI-QMS) and a reflectron time-of-flight mass spectrometer utilizing a photoionization source (PI-ReTOF-MS). Several previous in situ studies of ethylene ice irradiation using FTIR were substantiated with the detection of six products: [CH4 (CD4)], acetylene [C2H2 (C2D2)], the ethyl radical [C2H5 (C2D5)], ethane [C2H6 (C2D6)], 1-butene [C4H8 (C4D8)], and n-butane [C4H10 (C4D10)]. Contrary to previous gas phase studies, the PI-ReTOF-MS detected several groups of hydrocarbon with varying degrees of saturation: C n H2n+2 (n = 4-10), C n H2n (n = 2-12, 14, 16), C n H2n-2 (n = 3-12, 14, 16), C n H2n-4 (n = 4-12, 14, 16), C n H2n-6 (n = 4-10, 12), C n H2n-8 (n = 6-10), and C n H2n-10 (n = 6-10). Multiple laboratory studies have shown the facile production of ethylene from methane, which is a known ice constituent in the interstellar medium. Various astrophysically interesting molecules can be associated with the groups detected here, such as allene/methylacetylene (C3H4) or 1, 3-butadiene (C4H6) and its isomers, which have been shown to lead to polycyclic aromatic hydrocarbons. Finally, several hydrocarbon groups detected here are unique to ethylene ice versus ethane ice and may provide understanding of how complex hydrocarbons form in astrophysical environments.

Ellagitannin composition of blackberry as determined by HPLC-ESI-MS and MALDI-TOF-MS.

PubMed

Hager, Tiffany J; Howard, Luke R; Liyanage, Rohana; Lay, Jackson O; Prior, Ronald L

2008-02-13

Blackberries ( Rubus sp.) were evaluated by high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) to identify the ellagitannins present in flesh, torus (receptacle tissue), and seeds. Most ellagitannins were present (or detectable) only in seed tissues. Ellagitannins identified by HPLC-ESI-MS in the seeds included pedunculagin, casuarictin/potentillin, castalagin/vescalagin, lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D. For several of the ellagitannins, isomeric separation was also obtained. The MALDI-TOF-MS analysis was primarily utilized to evaluate and identify high molecular mass (>1000 Da) ellagitannins. The MALDI analysis verified the presence of the ellagitannins identified by HPLC-ESI-MS including lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D, but the analysis also indicated the presence of several other compounds that were most likely ellagitannins based on the patterns observed in the masses (i.e., loss or addition of a gallic acid moiety to a known ellagitannin). This study determined the presence of several possible isomeric forms of ellagitannins previously unidentified in fruit and presents a possible analytical HPLC method for the analysis of the major ellagitannins present in the fruit.

Differentiation of Staphylococcus argenteus (formerly: Staphylococcus aureus clonal complex 75) by mass spectrometry from S. aureus using the first strain isolated from a wild African great ape.

PubMed

Schuster, Dominik; Rickmeyer, Jasmin; Gajdiss, Mike; Thye, Thorsten; Lorenzen, Stephan; Reif, Marion; Josten, Michaele; Szekat, Christiane; Melo, Luís D R; Schmithausen, Ricarda M; Liégeois, Florian; Sahl, Hans-Georg; Gonzalez, Jean-Paul J; Nagel, Michael; Bierbaum, Gabriele

2017-01-01

The species Staphylococcus argenteus was separated recently from Staphylococcus aureus (Tong S.Y., F. Schaumburg, M.J. Ellington, J. Corander, B. Pichon, F. Leendertz, S.D. Bentley, J. Parkhill, D.C. Holt, G. Peters, and P.M. Giffard, 2015). The objective of this work was to characterise the genome of a non-human S. argenteus strain, which had been isolated from the faeces of a wild-living western lowland gorilla in Gabon, and analyse the spectrum of this species in matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The full genome sequence revealed a scarcity of virulence genes and absence of resistance genes, indicating a decreased virulence potential compared to S. aureus and the human methicillin-resistant S. argenteus isolate MSHR1132 T . Spectra obtained by MALDI-TOF MS and the analysis of available sequences in the genome databases identified several MALDI-TOF MS signals that clearly differentiate S. argenteus, the closely related Staphylococcus schweitzeri and S. aureus. In conclusion, in the absence of biochemical tests that identify the three species, mass spectrometry should be employed as method of choice. Copyright © 2016 Elsevier GmbH. All rights reserved.

Novel and simple route to fabricate fully biocompatible plasmonic mushroom arrays adhered on silk biopolymer

NASA Astrophysics Data System (ADS)

Park, Joonhan; Choi, Yunkyoung; Lee, Myungjae; Jeon, Heonsu; Kim, Sunghwan

2014-12-01

A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures.A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures. Electronic supplementary information (ESI) available: The incident angle dependence of reflectance spectra and the atomic force microscopy image of the Au nanoparticle array on a silk film after 1 hour of ultrasonication. See DOI: 10.1039/c4nr05172f

[Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

PubMed

Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

2014-01-01

The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Proteomic analysis of zebrafish embryos exposed to simulated-microgravity

NASA Astrophysics Data System (ADS)

Hang, Xiaoming; Ma, Wenwen; Wang, Wei; Liu, Cong; Sun, Yeqing

Microgravity can induce a serial of physiological and pathological changes in human body, such as cardiovascular functional disorder, bone loss, muscular atrophy and impaired immune system function, etc. In this research, we focus on the influence of microgravity to vertebrate embryo development. As a powerful model for studying vertebrate development, zebrafish embryos at 8 hpf (hour past fertilization) and 24 hpf were placed into a NASA developed bioreac-tor (RCCS) to simulate microgravity for 64 and 48 hours, respectively. The same number of control embryos from the same parents were placed in a tissue culture dish at the same temper-ature of 28° C. Each experiment was repeated 3 times and analyzed by two-dimensional (2-D) gel electrophoresis. Image analysis of silver stained 2-D gels revealed that 64 from total 292 protein spots showed quantitative and qualitative variations that were significantly (P<0.05) and reproducibly different between simulate-microgravity treatment and the stationary control samples. 4 protein spots with significant expression alteration (P<0.01) were excised from 2-D gels and analyzed by MALDI-TOF/TOF mass spectra primarily. Of these proteins, 3 down-regulated proteins were identified as bectin 2, centrosomal protein of 135kDa and tropomyosin 4, while the up-regulated protein was identified as creatine kinase muscle B. Other protein spots showed significant expression alteration will be identified successively and the corresponding genes expression will also be measured by Q-PCR method at different development stages. The data presented in this study illustrate that zebrafish embryo can be significantly induced by microgravity on the expression of proteins involved in bone and muscle formation. Key Words: Danio rerio; Simulated-microgravity; Proteomics

Metaproteomic analysis of biocake proteins to understand membrane fouling in a submerged membrane bioreactor.

PubMed

Zhou, Zhongbo; Meng, Fangang; He, Xiang; Chae, So-Ryong; An, Yujia; Jia, Xiaoshan

2015-01-20

Metaproteomic analyses, including two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) separation and matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)/TOF mass spectrometer (MS) detection, were used to trace and identify biocake proteins on membranes in a bench-scale submerged membrane bioreactor (MBR). 2D-PAGE images showed that proteins in the biocake (S3) at a low transmembrane pressure (TMP) level (i.e., before the TMP jump) had larger gray intensities in the pH 5.5–7.0 region regardless of the membrane flux, similar to soluble microbial product (SMP) proteins. However, the biocake (S2 and S4) at a high TMP level (i.e., after the TMP jump) had many more proteins in the pH range of 4.0–5.5, similar to extracellular polymeric substance (EPS) proteins. Such similarities between biocake proteins and SMP or EPS proteins can be useful for tracing the sources of proteins resulting in membrane fouling. In total, 183 differentially abundant protein spots were marked in the three biocakes (S2, S3, and S4). However, only 32 protein spots co-occurred in the 2D gels of the three biocakes, indicating that membrane fluxes and TMP evolution levels had significant effects on the abundance of biocake proteins. On the basis of the MS and MS/MS data, 23 of 71 protein spots were successfully identified. Of the 23 proteins, outer membrane proteins (Omp) were a major contributor (60.87%). These Omps were mainly from potential surface colonizers such as Aeromonas, Enterobacter, Pseudomonas, and Thauera. Generally, the metaproteomic analysis is a useful alternative to trace the sources and compositions of biocake proteins on the levels of molecules and bacteria species that can provide new insight into membrane fouling.

Impact of Time-of-Flight on PET Tumor Detection

PubMed Central

Kadrmas, Dan J.; Casey, Michael E.; Conti, Maurizio; Jakoby, Bjoern W.; Lois, Cristina; Townsend, David W.

2009-01-01

Time-of-flight (TOF) PET uses very fast detectors to improve localization of events along coincidence lines-of-response. This information is then utilized to improve the tomographic reconstruction. This work evaluates the effect of TOF upon an observer's performance for detecting and localizing focal warm lesions in noisy PET images. Methods An advanced anthropomorphic lesion-detection phantom was scanned 12 times over 3 days on a prototype TOF PET/CT scanner (Siemens Medical Solutions). The phantom was devised to mimic whole-body oncologic 18F-FDG PET imaging, and a number of spheric lesions (diameters 6–16 mm) were distributed throughout the phantom. The data were reconstructed with the baseline line-of-response ordered-subsets expectation-maximization algorithm, with the baseline algorithm plus point spread function model (PSF), baseline plus TOF, and with both PSF+TOF. The lesion-detection performance of each reconstruction was compared and ranked using localization receiver operating characteristics (LROC) analysis with both human and numeric observers. The phantom results were then subjectively compared to 2 illustrative patient scans reconstructed with PSF and with PSF+TOF. Results Inclusion of TOF information provides a significant improvement in the area under the LROC curve compared to the baseline algorithm without TOF data (P = 0.002), providing a degree of improvement similar to that obtained with the PSF model. Use of both PSF+TOF together provided a cumulative benefit in lesion-detection performance, significantly outperforming either PSF or TOF alone (P < 0.002). Example patient images reflected the same image characteristics that gave rise to improved performance in the phantom data. Conclusion Time-of-flight PET provides a significant improvement in observer performance for detecting focal warm lesions in a noisy background. These improvements in image quality can be expected to improve performance for the clinical tasks of detecting lesions and staging disease. Further study in a large clinical population is warranted to assess the benefit of TOF for various patient sizes and count levels, and to demonstrate effective performance in the clinical environment. PMID:19617317

Non-invasive ultrasonic technology for continuous monitoring of pork loin and ham dry salting.

PubMed

de Prados, Marta; Garcia-Perez, Jose V; Benedito, Jose

2017-06-01

Online ultrasound measurements were taken using pulse-echo mode in loins (Longissimus dorsi) and hams at different salting times (up to 30days). From the time-domain ultrasonic wave, the time of flight (TOF) was computed as well as its variation between two signals (ΔTOF). A progressive decrease in TOF during dry salting was found, which was linked to the salt gain, water loss and the reduction in sample thickness. Predictive models based on the ultrasonic parameters (ΔTOF and initial time of flight, TOF 0 ) correctly classified 85% of the loins and 90% of the hams into 3 groups of salt content (low/medium/high). The results obtained confirm that the use of the ultrasonic pulse-echo technique is of great potential in the non-destructive monitoring of dry salting in pork loins and hams, as well as in the prediction of the salt gain for classification purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

DIGE Analysis Software and Protein Identification Approaches.

PubMed

Hmmier, Abduladim; Dowling, Paul

2018-01-01

DIGE is a high-resolution two-dimensional gel electrophoresis method, with excellent dynamic range obtained by fluorescent tag labeling of protein samples. Scanned images of DIGE gels show thousands of protein spots, each spot representing a single or a group of protein isoforms. By using commercially available software, each protein spot is defined by an outline, which is digitized and correlated with the quantity of proteins present in each spot. Software packages include DeCyder, SameSpots, and Dymension 3. In addition, proteins of interest can be excised from post-stained gels and identified with conventional mass spectrometry techniques. High-throughput mass spectrometry is performed using sophisticated instrumentation including matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF), MALDI-TOF/TOF, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Tandem MS (MALDI-TOF/TOF or LC-MS/MS), analyzes fragmented peptides, resulting in amino acid sequence information, especially useful when protein spots are low abundant or where a mixture of proteins is present.

Automated High-Throughput Permethylation for Glycosylation Analysis of Biologics Using MALDI-TOF-MS.

PubMed

Shubhakar, Archana; Kozak, Radoslaw P; Reiding, Karli R; Royle, Louise; Spencer, Daniel I R; Fernandes, Daryl L; Wuhrer, Manfred

2016-09-06

Monitoring glycoprotein therapeutics for changes in glycosylation throughout the drug's life cycle is vital, as glycans significantly modulate the stability, biological activity, serum half-life, safety, and immunogenicity. Biopharma companies are increasingly adopting Quality by Design (QbD) frameworks for measuring, optimizing, and controlling drug glycosylation. Permethylation of glycans prior to analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is a valuable tool for glycan characterization and for screening of large numbers of samples in QbD drug realization. However, the existing protocols for manual permethylation and liquid-liquid extraction (LLE) steps are labor intensive and are thus not practical for high-throughput (HT) studies. Here we present a glycan permethylation protocol, based on 96-well microplates, that has been developed into a kit suitable for HT work. The workflow is largely automated using a liquid handling robot and includes N-glycan release, enrichment of N-glycans, permethylation, and LLE. The kit has been validated according to industry analytical performance guidelines and applied to characterize biopharmaceutical samples, including IgG4 monoclonal antibodies (mAbs) and recombinant human erythropoietin (rhEPO). The HT permethylation enabled glycan characterization and relative quantitation with minimal side reactions: the MALDI-TOF-MS profiles obtained were in good agreement with hydrophilic liquid interaction chromatography (HILIC) and ultrahigh performance liquid chromatography (UHPLC) data. Automated permethylation and extraction of 96 glycan samples was achieved in less than 5 h and automated data acquisition on MALDI-TOF-MS took on average less than 1 min per sample. This automated and HT glycan preparation and permethylation showed to be convenient, fast, and reliable and can be applied for drug glycan profiling and clinical glycan biomarker studies.

Novel and simple route to fabricate fully biocompatible plasmonic mushroom arrays adhered on silk biopolymer.

PubMed

Park, Joonhan; Choi, Yunkyoung; Lee, Myungjae; Jeon, Heonsu; Kim, Sunghwan

2015-01-14

A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures.

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast.

PubMed

Dhiman, Neelam; Hall, Leslie; Wohlfiel, Sherri L; Buckwalter, Seanne P; Wengenack, Nancy L

2011-04-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

Biosynthesis of staphylococcal enterotoxin A by genetic engineering technology and determination of staphylococcal enterotoxin A in water by HPLC-ESI-TOF.

PubMed

Li, Hong-Na; Yuan, Fei; Luo, Yun-Jing; Wang, Jian-Feng; Zhang, Chuan-Bin; Zhou, Wei-E; Ren, Zhi-Qin; Wu, Wen-Jie; Zhang, Feng

2017-08-01

Staphylococcal enterotoxin A (SEA) was the major virulence factor of Staphylococcus aureus and a biomarker of S. aureus. To establish a fast, low cost, high accuracy, reliable, and simple method for detecting S. aureus, SEA was analyzed by HPLC-ESI-TOF. SEA was not yet commercially available in universal, so SEA was prepared before it was analyzed by HPLC-ESI-TOF. The result showed that high purified SEA was successfully prepared and SEA has normal distribution in mass spectra. A large amount of recombinant SEA (rSEA) was obtained by engineering technology and was purified by Ni affinity chromatography column, and the expression and purity of rSEA and SEA were analyzed by SDS-PAGE. The factors effected on ionization of SEA were studied, and the qualitative analysis of SEA by HPLC-ESI-TOF. The result showed that large amount of SEs expressed within a short time at 28 °C or thereabouts, and there was no impurity bands in electrophorogram after rSEA was purified by Ni affinity chromatography column. In addition, the SEA which had homologous AA sequence with wild SEA was made by rSEA. The retention of SEA in column and ionization of SEA in ESI-TOF were studied for qualitative analysis of S. aureus. The result showed that the content of formic acid in mobile phase was an important factor for ionization of SEs in ESI-TOF. And the result provided theoretical foundation for qualitative detection of S. aureus. [SEs + nH + + mNH 4 + ] n+m+ was shown on ESI-TOF spectra when SEA was detected by ESI-TOF in positive ion mode, and the numerical value of n+m was less than or equal to the number of basic amino acids in SEs. This method was applied to determine SEA in water samples preliminarily, and the detection limit of SEA in spiked water sample was 3 mg/kg. The limit of detection of 3 mg/kg was low sensitivity for low molecular weight matters, but it was high sensitivity for SEA which had a high molecular weight of 27 kDa. Of SEA, 3 mg/kg was equivalent to 10 -4  mmol/kg of SEA. This study can provide evidence for establishing method to determine SEA in real samples.

Separation and characterization of chemical constituents in Ginkgo biloba extract by off-line hydrophilic interaction×reversed-phase two-dimensional liquid chromatography coupled with quadrupole-time of flight mass spectrometry.

PubMed

Ji, Shuai; He, Dan-Dan; Wang, Tian-Yun; Han, Jie; Li, Zheng; Du, Yan; Zou, Jia-Hui; Guo, Meng-Zhe; Tang, Dao-Quan

2017-11-30

Ginkgo biloba extract (GBE), derived from the leaves of Ginkgo biloba L., is one of the most widely used traditional Chinese medicines worldwide. Due to high structural diversity and low abundance of chemical constituents in GBE, conventional reversed-phase liquid chromatography has limited power to meet the needs of its quality control. In this study, an off-line hydrophilic interaction×reversed-phase two-dimensional liquid chromatography (HILIC×RP 2D-LC) system coupled with diode array detection (DAD) and quadrupole time-of-flight mass spectrometry (qTOF-MS) was established to comprehensively analyze the chemical constituents of GBE. After optimizing the chromatographic columns and mobile phase of 2D-LC, a Waters XBridge Amide column using acetonitrile/water/formic acid as the mobile phase was selected as the first dimension to fractionate GBE, and the obtained fractions were further separated on an Agilent Zorbax XDB-C18 column with methanol/water/formic acid as the mobile phase. As a result, a total of 125 compounds were detected in GBE. The orthogonality of the 2D-LC system was 69.5%, and the practical peak capacity was 3864 and 2994, respectively, calculated by two different methods. The structures of 104 compounds were tentatively characterized by qTOF-MS analysis, and 21 of them were further confirmed by comparing with reference standards. This established HILIC×RP 2D-LC-qTOF/MS system can greatly improve the separation and characterization of natural products in GBE or other complicated herbal extracts. Copyright © 2017 Elsevier B.V. All rights reserved.

Geometric investigation of a gaming active device

NASA Astrophysics Data System (ADS)

Menna, Fabio; Remondino, Fabio; Battisti, Roberto; Nocerino, Erica

2011-07-01

3D imaging systems are widely available and used for surveying, modeling and entertainment applications, but clear statements regarding their characteristics, performances and limitations are still missing. The VDI/VDE and the ASTME57 committees are trying to set some standards but the commercial market is not reacting properly. Since many new users are approaching these 3D recording methodologies, clear statements and information clarifying if a package or system satisfies certain requirements before investing are fundamental for those users who are not really familiar with these technologies. Recently small and portable consumer-grade active sensors came on the market, like TOF rangeimaging cameras or low-cost triangulation-based range sensor. A quite interesting active system was produced by PrimeSense and launched on the market thanks to the Microsoft Xbox project with the name of Kinect. The article reports the geometric investigation of the Kinect active sensors, considering its measurement performances, the accuracy of the retrieved range data and the possibility to use it for 3D modeling application.

Revealing the glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of Vibrio cholerae O1, serotype Ogawa with the BSA protein carrier using LC-ESI-QqTOF-MS/MS

PubMed Central

Jahouh, Farid; Saksena, Rina; Kováč, Pavol; Banoub, Joseph

2012-01-01

In this manuscript, we present the determination of glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of Vibrio cholerae O1 serotype Ogawa to BSA using nano- liquid chromatography electrospray ionization quadrupole time-of-flight tandem mass spectroscopy (LC-ESI-QqTOF-MS/MS). The matrix-assisted laser desorption/ionization-TOF/TOF-MS/MS analyses of the tryptic digests of the glycoconjugates having a hapten:BSA ratio of 4.3:1, 6.6:1 and 13.2:1 revealed only three glycation sites, on the following lysine residues: Lys 235, Lys 437 and Lys 455. Digestion of the neoglycoconjugates with the proteases trypsin and GluC V8 gave complementary structural information and was shown to maximize the number of recognized glycation sites. Here, we report identification of 20, 27 and 33 glycation sites using LC-ESI-QqTOF-MS/MS analysis of a series of synthetic neoglycoconjugates with a hapten:BSA ratio of, respectively, 4.3:1, 6.6:1 and 13.2:1. We also tentatively propose that all the glycated lysine residues are located mainly near the outer surface of the protein. PMID:22791257

Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry improves appropriateness of antibiotic treatment of bacteremia.

PubMed

Vlek, Anne L M; Bonten, Marc J M; Boel, C H Edwin

2012-01-01

Matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows the identification of microorganisms directly from positive blood culture broths. Use of the MALDI-TOF MS for rapid identification of microorganisms from blood culture broths can reduce the turnaround time to identification and may lead to earlier appropriate treatment of bacteremia. During February and April 2010, direct MALDI-TOF MS was routinely performed on all positive blood cultures. During December 2009 and March 2010 no direct MALDI-TOF MS was used. Information on antibiotic therapy was collected from the hospital and intensive care units' information systems from all positive blood cultures during the study period. In total, 253 episodes of bacteremia were included of which 89 during the intervention period and 164 during the control period. Direct performance of MALDI-TOF MS on positive blood culture broths reduced the time till species identification by 28.8-h and was associated with an 11.3% increase in the proportion of patients receiving appropriate antibiotic treatment 24 hours after blood culture positivity (64.0% in the control period versus 75.3% in the intervention period (p0.01)). Routine implementation of this technique increased the proportion of patients on adequate antimicrobial treatment within 24 hours.

Deep convolutional neural network and 3D deformable approach for tissue segmentation in musculoskeletal magnetic resonance imaging.

PubMed

Liu, Fang; Zhou, Zhaoye; Jang, Hyungseok; Samsonov, Alexey; Zhao, Gengyan; Kijowski, Richard

2018-04-01

To describe and evaluate a new fully automated musculoskeletal tissue segmentation method using deep convolutional neural network (CNN) and three-dimensional (3D) simplex deformable modeling to improve the accuracy and efficiency of cartilage and bone segmentation within the knee joint. A fully automated segmentation pipeline was built by combining a semantic segmentation CNN and 3D simplex deformable modeling. A CNN technique called SegNet was applied as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification. The 3D simplex deformable modeling refined the output from SegNet to preserve the overall shape and maintain a desirable smooth surface for musculoskeletal structure. The fully automated segmentation method was tested using a publicly available knee image data set to compare with currently used state-of-the-art segmentation methods. The fully automated method was also evaluated on two different data sets, which include morphological and quantitative MR images with different tissue contrasts. The proposed fully automated segmentation method provided good segmentation performance with segmentation accuracy superior to most of state-of-the-art methods in the publicly available knee image data set. The method also demonstrated versatile segmentation performance on both morphological and quantitative musculoskeletal MR images with different tissue contrasts and spatial resolutions. The study demonstrates that the combined CNN and 3D deformable modeling approach is useful for performing rapid and accurate cartilage and bone segmentation within the knee joint. The CNN has promising potential applications in musculoskeletal imaging. Magn Reson Med 79:2379-2391, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Penilumamide, a novel lumazine peptide isolated from the marine-derived fungus, Penicillium sp. CNL-338.

PubMed

Meyer, Sven W; Mordhorst, Thorsten F; Lee, Choonghwan; Jensen, Paul R; Fenical, William; Köck, Matthias

2010-05-07

A novel lumazine peptide, penilumamide (1), was isolated from the fermentation broth of a marine-derived fungal strain, identified as Penicillium sp. (strain CNL-338) and the structure of the new metabolite was determined by analysis of ESI-TOF MS data combined with 1D and 2D NMR experiments.

Probing Combustion Chemistry in a Miniature Shock Tube with Synchrotron VUV Photo Ionization Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lynch, Patrick T.; Troy, Tyler P.; Ahmed, Musahid

2015-01-29

Tunable synchrotron-sourced photoionization time-of-flight mass spectrometry (PI-TOF-MS) is an important technique in combustion chemistry, complementing lab-scale electron impact and laser photoionization studies for a wide variety of reactors, typically at low pressure. For high-temperature and high-pressure chemical kinetics studies, the shock tube is the reactor of choice. Extending the benefits of shock tube/TOF-MS research to include synchrotron sourced PI-TOF-MS required a radical reconception of the shock tube. An automated, miniature, high-repetition-rate shock tube was developed and can be used to study high-pressure reactive systems (T > 600 K, P < 100 bar) behind reflected shock waves. In this paper, wemore » present results of a PI-TOF-MS study at the Advanced Light Source at Lawrence Berkeley National Laboratory. Dimethyl ether pyrolysis (2% CH3OCH3/Ar) was observed behind the reflected shock (1400 < T-5 < 1700 K, 3 < P-5 < 16 bar) with ionization energies between 10 and 13 eV. Individual experiments have extremely low signal levels. However, product species and radical intermediates are well-resolved when averaging over hundreds of shots, which is ordinarily impractical in conventional shock tube studies. The signal levels attained and data throughput rates with this technique are comparable to those with other synchrotron-based PI-TOF-MS reactors, and it is anticipated that this high pressure technique will greatly complement those lower pressure techniques.« less

Growth inhibition of Candida species by Wickerhamomyces anomalus mycocin and a lactone compound of Aureobasidium pullulans.

PubMed

Tay, Sun-Tee; Lim, Su-Lin; Tan, Hui-Wee

2014-11-08

The increasing resistance of Candida yeasts towards antifungal compounds and the limited choice of therapeutic drugs have spurred great interest amongst the scientific community to search for alternative anti-Candida compounds. Mycocins and fungal metabolites have been reported to have the potential for treatment of fungal infections. In this study, the growth inhibition of Candida species by a mycocin produced by Wickerhamomyces anomalus and a lactone compound from Aureobasidium pullulans were investigated. Mycocin was purified from the culture supernatant of an environmental isolate of W. anomalus using Sephadex G-75 gel filtration column chromatography. The mycocin preparation was subjected to SDS-PAGE analysis followed by MALDI TOF/TOF mass spectrometry analysis. The thermal and temperature stability of the mycocin were determined. The glucanase activity of the mycocin was investigated by substrate staining of the mycocin with 4-methyl-umbelliferyl-ß-D-glucoside (MUG). Gas chromatography mass spectrometry (GCMS) analysis was used to identify anti-Candida metabolite in the culture supernatant of an environmental isolate of Aureobasidium pullulans. The inhibitory effects of the anti-Candida compound against planktonic and biofilm cultures of various Candida species were determined using broth microdilution and biofilm quantitation methods. A mycocin active against Candida mesorugosa but not C. albicans, C. parapsilosis and C. krusei was isolated from the culture supernatant of W. anomalus in this study. The mycocin, identified as exo-ß-1,3 glucanase by MALDI TOF/TOF mass spectrometry, was stable at pH 3-6 and temperature ranging from 4-37°C. The glucanase activity of the mycocin was confirmed by substrate staining with MUG. 5-hydroxy-2-decenoic acid lactone (HDCL) was identified from the culture supernatant of A. pullulans. Using a commercial source of HDCL, the planktonic and biofilm MICs of HDCL against various Candida species were determined in this study. W. anomalus mycocin demonstrated a narrow spectrum of activity targeting only against C. mesorugosa, while HDCL demonstrated a broad spectrum of inhibitory action against multiple Candida species. The growth inhibition of W. anomalus mycocin and the lactone compound from A. pullulans against Candida yeasts should be further explored for therapeutic potentials against candidiasis.

Identification of 14-3-3β in human gastric cancer cells and its potency as a diagnostic and prognostic biomarker.

PubMed

Tseng, Chien-Wei; Yang, Jyh-Chin; Chen, Chiung-Nien; Huang, Hsuan-Cheng; Chuang, Kai-Neng; Lin, Chen-Ching; Lai, Hong-Shiee; Lee, Po-Huang; Chang, King-Jen; Juan, Hsueh-Fen

2011-06-01

Gastric cancer is the second most common cause of cancer deaths worldwide and due to its poor prognosis, it is important that specific biomarkers are identified to enable its early detection. Through 2-D gel electrophoresis and MALDI-TOF-TOF-based proteomics approaches, we found that 14-3-3β, which was one of the proteins that were differentially expressed by 5-fluorouracil-treated gastric cancer SC-M1 cells, was upregulated in gastric cancer cells. 14-3-3β levels in tissues and serum were further validated in gastric cancer patients and controls. The results showed that 14-3-3β levels were elevated in tumor tissues (n=40) in comparison to normal tissues (n=40; p<0.01), and serum 14-3-3β levels in cancer patients (n=145) were also significantly higher than those in controls (n=63; p<0.0001). Elevated serum 14-3-3β levels highly correlated with the number of lymph node metastases, tumor size and a reduced survival rate. Moreover, overexpression of 14-3-3β enhanced the growth, invasiveness and migratory activities of tumor cells. Twenty-eight proteins involved in anti-apoptosis and tumor progression were also found to be differentially expressed in 14-3-3β-overexpressing gastric cancer cells. Overall, these results highlight the significance of 14-3-3β in gastric cancer cell progression and suggest that it has the potential to be used as a diagnostic and prognostic biomarker in gastric cancer. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ethylene hydrogenation catalysis on Pt(111) single-crystal surfaces studied by using mass spectrometry and in situ infrared absorption spectroscopy

NASA Astrophysics Data System (ADS)

Tillekaratne, Aashani; Simonovis, Juan Pablo; Zaera, Francisco

2016-10-01

The catalytic hydrogenation of ethylene promoted by a Pt(111) single crystal was studied by using a ultrahigh-vacuum surface-science instrument equipped with a so-called high-pressure cell. Kinetic data were acquired continuously during the catalytic conversion of atmospheric-pressure mixtures of ethylene and hydrogen by using mass spectrometry while simultaneously characterizing the surface species in operando mode by reflection-absorption infrared spectroscopy (RAIRS). Many observations reported in previous studies of this system were corroborated, including the presence of adsorbed alkylidyne intermediates during the reaction and the zero-order dependence of the rate of hydrogenation on the pressure of ethylene. In addition, the high quality of the kinetic data, which could be recorded continuously versus time and processed to calculate time-dependent turnover frequencies (TOFs), afforded a more detailed analysis of the mechanism. Specifically, deuterium labeling could be used to estimate the extent of isotope scrambling reached with mixed-isotope-substituted reactants (C2H4 + D2 and C2D4 + H2). Perhaps the most important new observation from this work is that, although extensive H-D exchange takes place on ethylene before being fully converted to ethane, the average stoichiometry of the final product retains the expected stoichiometry of the gas mixture, that is, four regular hydrogen atoms and two deuteriums per ethane molecule in the case of the experiments with C2H4 + D2. This means that no hydrogen atoms are removed from the surface via their inter-recombination to produce X2 (X = H or D). It is concluded that, under catalytic conditions, hydrogen surface recombination is much slower than ethylene hydrogenation and H-D exchange.

Evaluation of the site specific protein glycation and antioxidant capacity of rare sugar-protein/peptide conjugates.

PubMed

Sun, Yuanxia; Hayakawa, Shigeru; Ogawa, Masahiro; Izumori, Ken

2005-12-28

Protein-sugar conjugates generated in nonenzymatic glycation of alpha-lactalbumin (LA) with rare sugars [D-allose (All) and D-psicose (Psi)] and alimentary sugars as controls [D-glucose (Glc) and D-fructose (Fru)] were qualitatively determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Mass spectra revealed that the extent of glycation at lysine residues on LA with D-aldose molecules was very much higher than that of glycation with d-ketose molecules. To identify the specific site of glycation, the peptide mapping was established from protease V8 digestion, using a combination of computational cutting of proteins and MALDI-TOF-MS. As compared to peptide mapping, three and seven glycation sites were located in the primary structure of LA-ketose and LA-aldose conjugates, respectively. On the other hand, the antioxidant activities of protein-sugar conjugates and their peptic hydrolysates were investigated by 1,1-diphenyl-2-picrylhydrazyl radical scavenging method. The antioxidant activities of proteins/peptides glycated with rare sugars were significantly higher than those modified with the control sugars. The results indicated that the glycation degree and position were not markedly different between rare sugar and corresponding control sugar, but the antioxidant properties of protein and its hydrolysate were significantly enhanced by modifying with rare sugar.

Controlling Wafer Contamination Using Automated On-Line Metrology during Wet Chemical Cleaning

NASA Astrophysics Data System (ADS)

Wang, Jason; Kingston, Skip; Han, Ye; Saini, Harmesh; McDonald, Robert; Mui, Rudy

2003-09-01

The capabilities of a trace contamination analyzer are discussed and demonstrated. This analytical tool utilizes an electrospray, time-of-flight mass spectrometer (ES-TOF-MS) for fully automated on-line monitoring of wafer cleaning solutions. The analyzer provides rich information on metallic, anionic, cationic, elemental, and organic species through its ability to provide harsh (elemental) and soft (molecular) ionization under both positive and negative modes. It is designed to meet semiconductor process control and yield management needs for the ever increasing complex new chemistries present in wafer fabrication.

Synthesis of novel macrocycles carrying pincer-type ligands as future candidates for potential applications in size-selective, stereochemical and recyclable catalysts

NASA Astrophysics Data System (ADS)

Khan, Burhan; Shah, Muhammad Raza; Rabnawaz, Muhammad

2018-03-01

Macrocycles with ultra dense functionalities are very useful but are difficult to synthesize. In this study, we report six novel macrocycles bearing a pincer ligand alone or a combination of pincer-calixarenes, and pincer-fluorene moieties. Click chemistry was utilized to synthesize the desired macrocycles in good yields. These macrocycles were fully characterized using mass spectrometry (EI-MS, ESI-MS, and MALDI-TOF MS), and NMR spectroscopy. These macrocycles are under investigations as size-selective and recyclable catalysts for various chemical transformations.

Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

PubMed

Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

2013-12-19

To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

Ultra high field TOF-MRA: A method to visualize small cerebral vessels. 7T TOF-MRA sequence parameters on different MRI scanners - Literature review.

PubMed

Grochowski, Cezary; Staśkiewicz, Grzegorz

Time-of-flight (TOF) angiography is a technique allowing to visualize the blood flow in vessels. 7T ToF-MRA is able to visualize the whole Circle of Willis including small perforating branches without any known side effects as opposed to usually used DSA and CTA with high exposition to the radiation and high doses of contrast as far as CTA is concerned. The aim of this review is to describe ultra-high field ToF-MRA and present different protocol data depending on the scanner used in the study. PubMed, Embase, Ovid, Google Scholar databases were searched. Selection of studies for this systematic review included 7T magnetic resonance angiography studies. We searched for type of head coil used in various studies, flip angle, echo time, repetition time, field-of-view (FOV), number of slices per slab, matrix, voxel size and acquisition time. Visualization for the small perforating vessels of the Circle of Willis, that are not fully visualized using low-field-strength MRA is improving with increasing magnetic field strength, which has been proved by several studies. Ultra-high filed ToF-MRA has found to be a superior method in depicting cerebral microvasculature. 7T ToF-MRA seems to be a reliable method for visualization of arteries up to the second order cerebral arteries and has a potential to replace DSA. Copyright © 2017. Published by Elsevier Urban & Partner Sp. z o.o.

Nuclear data activities at the n_TOF facility at CERN

NASA Astrophysics Data System (ADS)

Gunsing, F.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Bacak, M.; Balibrea-Correa, J.; Barbagallo, M.; Barros, S.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Colonna, N.; Cortés-Giraldo, M. A.; Cortés, G.; Cosentino, L.; Damone, L. A.; Deo, K.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Frost, R. J. W.; Furman, V.; Ganesan, S.; García, A. R.; Gawlik, A.; Gheorghe, I.; Glodariu, T.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Griesmayer, E.; Guerrero, C.; Göbel, K.; Harada, H.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lerendegui, J.; Licata, M.; Lo Meo, S.; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Musumarra, A.; Nolte, R.; Oprea, A.; Palomo-Pinto, F. R.; Paradela, C.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Quesada, J. M.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Rout, P.; Radeck, D.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Stamatopoulos, A.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Weiss, C.; Wolf, C.; Woods, P. J.; Wright, T.; Žugec, P.

2016-10-01

Nuclear data in general, and neutron-induced reaction cross sections in particular, are important for a wide variety of research fields. They play a key role in the safety and criticality assessment of nuclear technology, not only for existing power reactors but also for radiation dosimetry, medical applications, the transmutation of nuclear waste, accelerator-driven systems, fuel cycle investigations and future reactor systems as in Generation IV. Applications of nuclear data are also related to research fields as the study of nuclear level densities and stellar nucleosynthesis. Simulations and calculations of nuclear technology applications largely rely on evaluated nuclear data libraries. The evaluations in these libraries are based both on experimental data and theoretical models. Experimental nuclear reaction data are compiled on a worldwide basis by the international network of Nuclear Reaction Data Centres (NRDC) in the EXFOR database. The EXFOR database forms an important link between nuclear data measurements and the evaluated data libraries. CERN's neutron time-of-flight facility n_TOF has produced a considerable amount of experimental data since it has become fully operational with the start of the scientific measurement programme in 2001. While for a long period a single measurement station (EAR1) located at 185 m from the neutron production target was available, the construction of a second beam line at 20 m (EAR2) in 2014 has substantially increased the measurement capabilities of the facility. An outline of the experimental nuclear data activities at CERN's neutron time-of-flight facility n_TOF will be presented.

Comparison of PCR/Electron spray Ionization-Time-of-Flight-Mass Spectrometry versus Traditional Clinical Microbiology for active surveillance of organisms contaminating high-use surfaces in a burn intensive care unit, an orthopedic ward and healthcare workers

PubMed Central

2012-01-01

Background Understanding nosocomial pathogen transmission is restricted by culture limitations. Novel platforms, such as PCR-based electron spray ionization-time-of-flight-mass spectrometry (ESI-TOF-MS), may be useful as investigational tools. Methods Traditional clinical microbiology (TCM) and PCR/ESI-TOF-MS were used to recover and detect microorganisms from the hands and personal protective equipment of 10 burn intensive care unit (ICU) healthcare workers providing clinical care at a tertiary care military referral hospital. High-use environmental surfaces were assessed in 9 burn ICU and 10 orthopedic patient rooms. Clinical cultures during the study period were reviewed for pathogen comparison with investigational molecular diagnostic methods. Results From 158 samples, 142 organisms were identified by TCM and 718 by PCR/ESI-TOF-MS. The molecular diagnostic method detected more organisms (4.5 ± 2.1 vs. 0.9 ± 0.8, p < 0.01) from 99% vs. 67% of samples (p < 0.01). TCM detected S. aureus in 13 samples vs. 21 by PCR/ESI-TOF-MS. Gram-negative organisms were less commonly identified than gram-positive by both methods; especially by TCM. Among all detected bacterial species, similar percentages were typical nosocomial pathogens (18-19%) for TCM vs. PCR/ESI-TOF-MS. PCR/ESI-TOF-MS also detected mecA in 112 samples, vanA in 13, and KPC-3 in 2. MecA was associated (p < 0.01) with codetection of coagulase negative staphylococci but not S. aureus. No vanA was codetected with enterococci; one KPC-3 was detected without Klebsiella spp. Conclusions In this pilot study, PCR/ESI-TOF-MS detected more organisms, especially gram-negatives, compared to TCM, but the current assay format is limited by the number of antibiotic resistance determinants it covers. Further large-scale assessments of PCR/ESI-TOF-MS for hospital surveillance are warranted. PMID:23050585

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry-based blood group genotyping--the alternative approach.

PubMed

Gassner, Christoph; Meyer, Stefan; Frey, Beat M; Vollmert, Caren

2013-01-01

Although matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry (MALDI-TOF MS) has previously been reported for high throughput blood group genotyping, those reports are limited to only a few blood group systems. This review describes the development of a large cooperative Swiss-German project, aiming to employ MALDI-TOF MS for the molecular detection of the blood groups Rh, Kell, Kidd, Duffy, MNSs, a comprehensive collection of low incidence antigens, as well as the platelet and granulocyte antigens HPA and HNA, representing a total of 101 blood group antigens, encoded by 170 alleles, respectively. Recent reports describe MALDI-TOF MS as a technology with short time-to-resolution, ability for high throughput, and cost-efficiency when used in genetic analysis, including forensics, pharmacogenetics, oncology and hematology. Furthermore, Kell and RhD genotyping have been performed on fetal DNA from maternal plasma with excellent results. In summary, this article introduces a new technological approach for high throughput blood group genotyping by means of MALDI-TOF MS. Although all data presented are preliminary, the observed success rates, data quality and concordance with known blood group types are highly impressive, underlining the accuracy and reliability of this cost-efficient high throughput method. Copyright © 2013 Elsevier Inc. All rights reserved.

Fully automated, real-time 3D ultrasound segmentation to estimate first trimester placental volume using deep learning.

PubMed

Looney, Pádraig; Stevenson, Gordon N; Nicolaides, Kypros H; Plasencia, Walter; Molloholli, Malid; Natsis, Stavros; Collins, Sally L

2018-06-07

We present a new technique to fully automate the segmentation of an organ from 3D ultrasound (3D-US) volumes, using the placenta as the target organ. Image analysis tools to estimate organ volume do exist but are too time consuming and operator dependant. Fully automating the segmentation process would potentially allow the use of placental volume to screen for increased risk of pregnancy complications. The placenta was segmented from 2,393 first trimester 3D-US volumes using a semiautomated technique. This was quality controlled by three operators to produce the "ground-truth" data set. A fully convolutional neural network (OxNNet) was trained using this ground-truth data set to automatically segment the placenta. OxNNet delivered state-of-the-art automatic segmentation. The effect of training set size on the performance of OxNNet demonstrated the need for large data sets. The clinical utility of placental volume was tested by looking at predictions of small-for-gestational-age babies at term. The receiver-operating characteristics curves demonstrated almost identical results between OxNNet and the ground-truth). Our results demonstrated good similarity to the ground-truth and almost identical clinical results for the prediction of SGA.

Lattice Boltzmann Method for 3-D Flows with Curved Boundary

NASA Technical Reports Server (NTRS)

Mei, Renwei; Shyy, Wei; Yu, Dazhi; Luo, Li-Shi

2002-01-01

In this work, we investigate two issues that are important to computational efficiency and reliability in fluid dynamics applications of the lattice, Boltzmann equation (LBE): (1) Computational stability and accuracy of different lattice Boltzmann models and (2) the treatment of the boundary conditions on curved solid boundaries and their 3-D implementations. Three athermal 3-D LBE models (D3QI5, D3Ql9, and D3Q27) are studied and compared in terms of efficiency, accuracy, and robustness. The boundary treatment recently developed by Filippova and Hanel and Met et al. in 2-D is extended to and implemented for 3-D. The convergence, stability, and computational efficiency of the 3-D LBE models with the boundary treatment for curved boundaries were tested in simulations of four 3-D flows: (1) Fully developed flows in a square duct, (2) flow in a 3-D lid-driven cavity, (3) fully developed flows in a circular pipe, and (4) a uniform flow over a sphere. We found that while the fifteen-velocity 3-D (D3Ql5) model is more prone to numerical instability and the D3Q27 is more computationally intensive, the 63Q19 model provides a balance between computational reliability and efficiency. Through numerical simulations, we demonstrated that the boundary treatment for 3-D arbitrary curved geometry has second-order accuracy and possesses satisfactory stability characteristics.

AFRRI Reports, First Quarter 1993

DTIC Science & Technology

1993-05-01

Oncology, Southern Califbrnia Sonw oifI these dlifferenles a rt: t hat, !or these Ia te Cancer Research Labo~ratory, U1Tniversity of’Southern Calilor- (fetp...acid WXR- 1065, lot BK 71 365 vas ob~taine’d fro nt I ndependently, the protective efh(’cts tof ’AR-151326 the )i~vision of’ Cancer Treatmniit...ion nttr one drn ativ kithbi . Cancer Rewarrauh. 45, 5-3 79-538 1. References ti’.~PRATNOr C~., 198.51h. ’’llre radii rotiriie~t’ r XVRI 065 Reeecsred

Inhalation Toxicology. 4. Times to Incapacitation and Death for Rats Exposed Continuously to Atmospheric Hydrogen Chloride Gas

DTIC Science & Technology

1985-05-01

Governrent Accession No. 3. Recipient’s Cutalog No. "FAA-AM-85-P i 4. Title and Subtitle 5. Report Date Inhalation Toxicology : IV. Times To...reported for humans is discuss dA.erin7o r I F. I 17. Key Words Di Ostribution Statement ."Combustion toxicology ; Smoke, Irritant ’Diocument is available to...F 1700.7 (8-72) Reproduction of completed page authorized INHALATION TOXICOLOGY : IV. TIMES TO INCAPACITATION AND DEATH FOR RATS EXPOSED CONTINUOUSLY

3D image processing architecture for camera phones

NASA Astrophysics Data System (ADS)

Atanassov, Kalin; Ramachandra, Vikas; Goma, Sergio R.; Aleksic, Milivoje

2011-03-01

Putting high quality and easy-to-use 3D technology into the hands of regular consumers has become a recent challenge as interest in 3D technology has grown. Making 3D technology appealing to the average user requires that it be made fully automatic and foolproof. Designing a fully automatic 3D capture and display system requires: 1) identifying critical 3D technology issues like camera positioning, disparity control rationale, and screen geometry dependency, 2) designing methodology to automatically control them. Implementing 3D capture functionality on phone cameras necessitates designing algorithms to fit within the processing capabilities of the device. Various constraints like sensor position tolerances, sensor 3A tolerances, post-processing, 3D video resolution and frame rate should be carefully considered for their influence on 3D experience. Issues with migrating functions such as zoom and pan from the 2D usage model (both during capture and display) to 3D needs to be resolved to insure the highest level of user experience. It is also very important that the 3D usage scenario (including interactions between the user and the capture/display device) is carefully considered. Finally, both the processing power of the device and the practicality of the scheme needs to be taken into account while designing the calibration and processing methodology.

Usefulness and accuracy of MALDI-TOF mass spectrometry as a supplementary tool to identify mosquito vector species and to invest in development of international database.

PubMed

Raharimalala, F N; Andrianinarivomanana, T M; Rakotondrasoa, A; Collard, J M; Boyer, S

2017-09-01

Arthropod-borne diseases are important causes of morbidity and mortality. The identification of vector species relies mainly on morphological features and/or molecular biology tools. The first method requires specific technical skills and may result in misidentifications, and the second method is time-consuming and expensive. The aim of the present study is to assess the usefulness and accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a supplementary tool with which to identify mosquito vector species and to invest in the creation of an international database. A total of 89 specimens belonging to 10 mosquito species were selected for the extraction of proteins from legs and for the establishment of a reference database. A blind test with 123 mosquitoes was performed to validate the MS method. Results showed that: (a) the spectra obtained in the study with a given species differed from the spectra of the same species collected in another country, which highlights the need for an international database; (b) MALDI-TOF MS is an accurate method for the rapid identification of mosquito species that are referenced in a database; (c) MALDI-TOF MS allows the separation of groups or complex species, and (d) laboratory specimens undergo a loss of proteins compared with those isolated in the field. In conclusion, MALDI-TOF MS is a useful supplementary tool for mosquito identification and can help inform vector control. © 2017 The Royal Entomological Society.

Time-resolved imaging of contrast kinetics does not improve performance of follow-up MRA of embolized intracranial aneurysms.

PubMed

Serafin, Zbigniew; Strześniewski, Piotr; Lasek, Władysław; Beuth, Wojciech

2012-07-01

The use of contrast media and the time-resolved imaging of contrast kinetics (TRICKS) technique have some theoretical advantages over time-of-flight magnetic resonance angiography (TOF-MRA) in the follow-up of intracranial aneurysms after endovascular treatment. We prospectively compared the diagnostic performance of TRICKS and TOF-MRA with digital subtracted angiography (DSA) in the assessment of occlusion of embolized aneurysms. Seventy-two consecutive patients with 72 aneurysms were examined 3 months after embolization. Test characteristics of TOF-MRA and TRICKS were calculated for the detection of residual flow. The results of quantification of flow were compared with weighted kappa. Intraobserver and interobserver reproducibility was determined. The sensitivity of TOF-MRA was 85% (95% CI, 65-96%) and of TRICKS, 89% (95% CI, 70-97%). The specificity of both methods was 91% (95% CI, 79-98%). The accuracy of the flow quantification ranged from 0.76 (TOF-MRA) to 0.83 (TRICKS). There was no significant difference between the methods in the area under the ROC curve regarding both the detection and the quantification of flow. Intraobserver reproducibility was very good with both techniques (kappa, 0.86-0.89). The interobserver reproducibility was moderate for TOF-MRA and very good for TRICKS (kappa, 0.74-0.80). In this study, TOF-MRA and TRICKS presented similar diagnostic performance; therefore, the use of time-resolved contrast-enhanced MRA is not justified in the follow-up of embolized aneurysms.

Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for the identification of Neisseria gonorrhoeae.

PubMed

Buchanan, R; Ball, D; Dolphin, H; Dave, J

2016-09-01

Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared with the API NH biochemical method for the identification of Neisseria gonorrhoeae in routine clinical samples. A retrospective review of laboratory records for 1090 isolates for which both biochemical and MALDI-TOF MS identifications were available was performed. Cases of discrepant results were examined in detail for evidence supportive of a particular organism identification. Of 1090 isolates, 1082 were identified as N. gonorrhoeae by API NH. MALDI-TOF MS successfully identified 984 (91%) of these after one analysis, rising to 1081 (99.9%) after two analyses, with a positive predictive value of 99.3%. For those isolates requiring a repeat analysis, failure to generate an identifiable proteomic signature was the reason in 76% of cases, with alternative initial identifications accounting for the remaining 24%. MALDI-TOF MS identified eight isolates as N. gonorrhoeae that were not identified as such by API NH-examination of these discrepant results suggested that the MALDI-TOF MS identification may be the more reliable. MALDI-TOF MS is at least as accurate and reliable a method of identifying N. gonorrhoeae as API NH. We propose that MALDI-TOF MS could potentially be used as a single method for N. gonorrhoeae identification in routine cases by laboratories with access to this technology. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

[Application of MALDI-TOF-MS in gene testing for non-syndromic hearing loss].

PubMed

Zeng, Yun; Jiang, Dan; Feng, Da-fei; Jin, Dong-dong; Wu, Xiao-hui; Ding, Yan-li; Zou, Jing

2013-12-01

To investigate the feasibility of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) , according to the genetic test of non-syndromic hearing loss (NSHL), and check using the direct sequencing. Peripheral blood was collected from 454 NSHL patients. DNA samples were extracted and 20 loci of the four common disease-causing genes were analysed by MALDI-TOF-MS, including GJB2 (35delG, 167delT, 176_191del16, 235delC, 299_300delAT ), GJB3 (538C→T, 547G→A), SLC26A4 (281C→T, 589G→A, IVS7-2A→G, 1174A→T, 1226G→A, 1229C→T, IVS15+5G→A, 1975G→C, 2027T→A, 2162C→T, 2168A→G), and mitochondrial 12S rRNA (1494C→T, 1555A→G). Direct sequencing was also used to analyse the aforementioned 20 loci in order to validate the accuracy of MALDI-TOF-MS. Among the 454 patients, 166 cases (36.56%) of disease-causing mutations were detected, which included 69 cases (21.15%) of GJB2 gene mutation, four cases (0.88%) of GJB3 gene mutation, 64 cases (14.10%) of SLC26A4 gene mutation, and three cases (0.66%) of mitochondrial 12S rRNA gene mutation. Moreover, the results obtained from direct sequencing and MALDI-TOF-MS were consistent, and the results showed that the two methods were consistent. The MALDI-TOF-MS detection method was designed based on the hearing loss-related mutation hotspots seen in the Chinese population, and it has a high detection rate for NSHL related mutations. In comparison to the conventional detection methods, MALDI-TOF-MS has the following advantages: more detection sites, greater coverage, accurate, high throughput and low cost. Therefore, this method is capable of satisfying the needs of clinical detection for hearing impairment and it is suitable for large-scale implementation.

Quantitative evaluation of high intensity signal on MIP images of carotid atherosclerotic plaques from routine TOF-MRA reveals elevated volumes of intraplaque hemorrhage and lipid rich necrotic core.

PubMed

Yamada, Kiyofumi; Song, Yan; Hippe, Daniel S; Sun, Jie; Dong, Li; Xu, Dongxiang; Ferguson, Marina S; Chu, Baocheng; Hatsukami, Thomas S; Chen, Min; Zhou, Cheng; Yuan, Chun

2012-11-29

Carotid intraplaque hemorrhage (IPH) and lipid rich necrotic core (LRNC) have been associated with accelerated plaque growth, luminal narrowing, future surface disruption and development of symptomatic events. The aim of this study was to evaluate the quantitative relationships between high intensity signals (HIS) in the plaque on TOF-MRA and IPH or LRNC volumes as measured by multicontrast weighted CMR. Seventy six patients with a suspected carotid artery stenosis or carotid plaque by ultrasonography underwent multicontrast carotid CMR. HIS presence and volume were measured from TOF-MRA MIP images while IPH and LRNC volumes were separately measured from multicontrast CMR. For detecting IPH, HIS on MIP images overall had high specificity (100.0%, 95% CI: 93.0 - 100.0%) but relatively low sensitivity (32%, 95% CI: 20.8 - 47.9%). However, the sensitivity had a significant increasing relationship with underlying IPH volume (p = 0.033) and degree of stenosis (p = 0.022). Mean IPH volume was 2.7 times larger in those with presence of HIS than in those without (142.8 ± 97.7 mm(3) vs. 53.4 ± 56.3 mm(3), p = 0.014). Similarly, mean LRNC volume was 3.4 times larger in those with HIS present (379.8 ± 203.4 mm(3) vs. 111.3 ± 122.7 mm(3), p = 0.001). There was a strong correlation between the volume of the HIS region and the IPH volume measured from multicontrast CMR (r = 0.96, p < 0.001). MIP images are easily reformatted from three minute, routine, clinical TOF sequences. High intensity signals in carotid plaque on TOF-MRA MIP images are associated with increased intraplaque hemorrhage and lipid-rich necrotic core volumes. The technique is most sensitive in patients with moderate to severe stenosis.

Adaptive bilateral filter for image denoising and its application to in-vitro Time-of-Flight data

NASA Astrophysics Data System (ADS)

Seitel, Alexander; dos Santos, Thiago R.; Mersmann, Sven; Penne, Jochen; Groch, Anja; Yung, Kwong; Tetzlaff, Ralf; Meinzer, Hans-Peter; Maier-Hein, Lena

2011-03-01

Image-guided therapy systems generally require registration of pre-operative planning data with the patient's anatomy. One common approach to achieve this is to acquire intra-operative surface data and match it to surfaces extracted from the planning image. Although increasingly popular for surface generation in general, the novel Time-of-Flight (ToF) technology has not yet been applied in this context. This may be attributed to the fact that the ToF range images are subject to considerable noise. The contribution of this study is two-fold. Firstly, we present an adaption of the well-known bilateral filter for denoising ToF range images based on the noise characteristics of the camera. Secondly, we assess the quality of organ surfaces generated from ToF range data with and without bilateral smoothing using corresponding high resolution CT data as ground truth. According to an evaluation on five porcine organs, the root mean squared (RMS) distance between the denoised ToF data points and the reference computed tomography (CT) surfaces ranged from 3.0 mm (lung) to 9.0 mm (kidney). This corresponds to an error-reduction of up to 36% compared to the error of the original ToF surfaces.

Imaging performance of a LaBr3-based PET scanner

PubMed Central

Daube-Witherspoon, M E; Surti, S; Perkins, A; Kyba, C C M; Wiener, R; Werner, M E; Kulp, R; Karp, J S

2010-01-01

A prototype time-of-flight (TOF) PET scanner based on cerium-doped lanthanum bromide [LaBr3 (5% Ce)] has been developed. LaBr3 has high light output, excellent energy resolution, and fast timing properties that have been predicted to lead to good image quality. Intrinsic performance measurements of spatial resolution, sensitivity, and scatter fraction demonstrate good conventional PET performance; the results agree with previous simulation studies. Phantom measurements show the excellent image quality achievable with the prototype system. Phantom measurements and corresponding simulations show a faster and more uniform convergence rate, as well as more uniform quantification, for TOF reconstruction of the data, which have 375-ps intrinsic timing resolution, compared to non-TOF images. Measurements and simulations of a hot and cold sphere phantom show that the 7% energy resolution helps to mitigate residual errors in the scatter estimate because a high energy threshold (>480 keV) can be used to restrict the amount of scatter accepted without a loss of true events. Preliminary results with incorporation of a model of detector blurring in the iterative reconstruction algorithm show improved contrast recovery but also point out the importance of an accurate resolution model of the tails of LaBr3’s point spread function. The LaBr3 TOF-PET scanner has demonstrated the impact of superior timing and energy resolutions on image quality. PMID:19949259

Ultra-low-loss tapered optical fibers with minimal lengths

NASA Astrophysics Data System (ADS)

Nagai, Ryutaro; Aoki, Takao

2014-11-01

We design and fabricate ultra-low-loss tapered optical fibers (TOFs) with minimal lengths. We first optimize variations of the torch scan length using the flame-brush method for fabricating TOFs with taper angles that satisfy the adiabaticity criteria. We accordingly fabricate TOFs with optimal shapes and compare their transmission to TOFs with a constant taper angle and TOFs with an exponential shape. The highest transmission measured for TOFs with an optimal shape is in excess of 99.7 % with a total TOF length of only 23 mm, whereas TOFs with a constant taper angle of 2 mrad reach 99.6 % transmission for a 63 mm TOF length.

Fourier-Domain Shift Matching: A Robust Time-of-Flight Approach for Shear Wave Speed Estimation.

PubMed

Rosen, David; Jiang, Jingfeng

2018-05-01

Our primary objective of this work was to design and test a new time-of-flight (TOF) method that allows measurements of shear wave speed (SWS) following impulsive excitation in soft tissues. Particularly, under the assumption of the local plane shear wave, this work named the Fourier-domain shift matching (FDSM) method, estimates SWS by aligning a series of shear waveforms either temporally or spatially using a solution space deduced by characteristic curves of the well-known 1-D wave equation. The proposed SWS estimation method was tested using computer-simulated data, and tissue-mimicking phantom and ex vivo tissue experiments. Its performance was then compared with three other known TOF methods: lateral time-to-peak (TTP) method with robust random sampling consensus (RANSAC) fitting method, Radon sum transformation method, and a modified cross correlation method. Hereafter, these three TOF methods are referred to as the TTP-RANSAC, Radon sum, and X-corr methods, respectively. In addition to an adapted form of the 2-D Fourier transform (2-D FT)-based method in which the (group) SWS was approximated by averaging phase SWS values was considered for comparison. Based on data evaluated, we found that the overall performance of the above-mentioned temporal implementation of the proposed FDSM method was most similar to the established Radon sum method (correlation = 0.99, scale factor = 1.03, and mean difference = 0.07 m/s), and the 2-D FT (correlation = 0.98, scale factor = 1.00, and mean difference = 0.10 m/s) at high signal quality. However, results obtained from the 2-D FT method diverged (correlation = 0.201) from these of the proposed temporal implementation in the presence of diminished signal quality, whereas the agreement between the Radon sum approach and the proposed temporal implementation largely remained the same (correlation = 0.98).

Clinical evaluation of whole-body oncologic PET with time-of-flight and point-spread function for the hybrid PET/MR system.

PubMed

Shang, Kun; Cui, Bixiao; Ma, Jie; Shuai, Dongmei; Liang, Zhigang; Jansen, Floris; Zhou, Yun; Lu, Jie; Zhao, Guoguang

2017-08-01

Hybrid positron emission tomography/magnetic resonance (PET/MR) imaging is a new multimodality imaging technology that can provide structural and functional information simultaneously. The aim of this study was to investigate the effects of the time-of-flight (TOF) and point-spread function (PSF) on small lesions observed in PET/MR images from clinical patient image sets. This study evaluated 54 small lesions in 14 patients who had undergone 18 F-fluorodeoxyglucose (FDG) PET/MR. Lesions up to 30mm in diameter were included. The PET data were reconstructed with a baseline ordered-subsets expectation-maximization (OSEM) algorithm, OSEM+PSF, OSEM+TOF and OSEM+TOF+PSF. PET image quality and small lesions were visually evaluated and scored by a 3-point scale. A quantitative analysis was then performed using the mean and maximum standardized uptake value (SUV) of the small lesions (SUV mean and SUV max ). The lesions were divided into two groups according to the long-axis diameter and the location respectively and evaluated with each reconstruction algorithm. We also evaluated the background signal by analyzing the SUV liver . OSEM+TOF+PSF provided the highest value and OSEM+TOF or PSF showed a higher value than OSEM for the visual assessment and quantitative analysis. The combination of TOF and PSF increased the SUV mean by 26.6% and the SUV max by 30.0%. The SUV liver was not influenced by PSF or TOF. For the OSEM+TOF+PSF model, the change in SUV mean and SUV max for lesions <10mm in diameter was 31.9% and 35.8%, and 24.5% and 27.6% for lesions 10-30mm in diameter, respectively. The abdominal lesions obtained the higher SUV than those of chest on the images with TOF and/or PSF. Application of TOF and PSF significantly increased the SUV of small lesions in hybrid PET/MR images, potentially improving small lesion detectability. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method.

PubMed

Costa-Alcalde, José Javier; Barbeito-Castiñeiras, Gema; González-Alba, José María; Aguilera, Antonio; Galán, Juan Carlos; Pérez-Del-Molino, María Luisa

2018-06-02

The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method. We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType ® CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial rpoβ gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank. The degree of agreement between GenoType ® and MALDI-TOF MS and the reference method, partial rpoβ sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType ® , we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType ® had misclassified (p=0.005). MALDI-TOF MS classified significantly better than GenoType ® . When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial rpoβ gene sequencing were equivalent. GenoType ® was not able to distinguish between species belonging to the M. fortuitum complex. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType ® . The partial rpoβ sequencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Evaluation of post-surgical cognitive function and protein fingerprints in the cerebro-spinal fluid utilizing surface-enhanced laser Desorption/Ionization time-of-flight mass-spectrometry (SELDI-TOF MS) after coronary artery bypass grafting: review of proteomic analytic tools and introducing a new syndrome.

PubMed

Reis, H J; Wang, L; Verano-Braga, T; Pimenta, A M C; Kálmán, J; Bogáts, G; Babik, B; Vieira, L B; Teixeira, A L; Mukhamedyarov, M A; Zefirov, A L; Kiyasov, A P; Rizvanov, A A; Matin, K; Palotás, M; Guimarães, M M; Ferreira, C N; Yalvaç, M E; Janka, Z; Palotás, A

2011-01-01

Cognitive dysfunction following surgery is a common complication, which increases the incidence of other co-morbid conditions, hospital and health-care costs. The reported rate of the occurrence of post-operative cognitive decline varies with different studies, depending on population profile, type of surgery, definition of cognitive disorder and detection methods, design of study, etc. It remains unclear whether these psychiatric signs and symptoms are direct results of the effects of surgery or general anesthesia. Nonetheless they are more frequent after cardiac surgery and are likely to be multi-factorial, but the patho-mechanisms are not yet fully characterized. This communication provides a synopsis of proteomics tools and delineates novel SELDI-TOF results to evaluate biomarkers in this regard. Presented for the first time is a classification of the clinically relevant forms of post-operative cognitive decline with the advent of a novel subclass.

Proteomic Analysis of Saliva Identifies Potential Biomarkers for Orthodontic Tooth Movement

PubMed Central

Ellias, Mohd Faiz; Zainal Ariffin, Shahrul Hisham; Karsani, Saiful Anuar; Abdul Rahman, Mariati; Senafi, Shahidan; Megat Abdul Wahab, Rohaya

2012-01-01

Orthodontic treatment has been shown to induce inflammation, followed by bone remodelling in the periodontium. These processes trigger the secretion of various proteins and enzymes into the saliva. This study aims to identify salivary proteins that change in expression during orthodontic tooth movement. These differentially expressed proteins can potentially serve as protein biomarkers for the monitoring of orthodontic treatment and tooth movement. Whole saliva from three healthy female subjects were collected before force application using fixed appliance and at 14 days after 0.014′′ Niti wire was applied. Salivary proteins were resolved using two-dimensional gel electrophoresis (2DE) over a pH range of 3–10, and the resulting proteome profiles were compared. Differentially expressed protein spots were then identified by MALDI-TOF/TOF tandem mass spectrometry. Nine proteins were found to be differentially expressed; however, only eight were identified by MALDI-TOF/TOF. Four of these proteins—Protein S100-A9, immunoglobulin J chain, Ig alpha-1 chain C region, and CRISP-3—have known roles in inflammation and bone resorption. PMID:22919344

List-mode reconstruction for the Biograph mCT with physics modeling and event-by-event motion correction

NASA Astrophysics Data System (ADS)

Jin, Xiao; Chan, Chung; Mulnix, Tim; Panin, Vladimir; Casey, Michael E.; Liu, Chi; Carson, Richard E.

2013-08-01

Whole-body PET/CT scanners are important clinical and research tools to study tracer distribution throughout the body. In whole-body studies, respiratory motion results in image artifacts. We have previously demonstrated for brain imaging that, when provided with accurate motion data, event-by-event correction has better accuracy than frame-based methods. Therefore, the goal of this work was to develop a list-mode reconstruction with novel physics modeling for the Siemens Biograph mCT with event-by-event motion correction, based on the MOLAR platform (Motion-compensation OSEM List-mode Algorithm for Resolution-Recovery Reconstruction). Application of MOLAR for the mCT required two algorithmic developments. First, in routine studies, the mCT collects list-mode data in 32 bit packets, where averaging of lines-of-response (LORs) by axial span and angular mashing reduced the number of LORs so that 32 bits are sufficient to address all sinogram bins. This degrades spatial resolution. In this work, we proposed a probabilistic LOR (pLOR) position technique that addresses axial and transaxial LOR grouping in 32 bit data. Second, two simplified approaches for 3D time-of-flight (TOF) scatter estimation were developed to accelerate the computationally intensive calculation without compromising accuracy. The proposed list-mode reconstruction algorithm was compared to the manufacturer's point spread function + TOF (PSF+TOF) algorithm. Phantom, animal, and human studies demonstrated that MOLAR with pLOR gives slightly faster contrast recovery than the PSF+TOF algorithm that uses the average 32 bit LOR sinogram positioning. Moving phantom and a whole-body human study suggested that event-by-event motion correction reduces image blurring caused by respiratory motion. We conclude that list-mode reconstruction with pLOR positioning provides a platform to generate high quality images for the mCT, and to recover fine structures in whole-body PET scans through event-by-event motion correction.

Micro-optical system based 3D imaging for full HD depth image capturing

NASA Astrophysics Data System (ADS)

Park, Yong-Hwa; Cho, Yong-Chul; You, Jang-Woo; Park, Chang-Young; Yoon, Heesun; Lee, Sang-Hun; Kwon, Jong-Oh; Lee, Seung-Wan

2012-03-01

20 Mega-Hertz-switching high speed image shutter device for 3D image capturing and its application to system prototype are presented. For 3D image capturing, the system utilizes Time-of-Flight (TOF) principle by means of 20MHz high-speed micro-optical image modulator, so called 'optical shutter'. The high speed image modulation is obtained using the electro-optic operation of the multi-layer stacked structure having diffractive mirrors and optical resonance cavity which maximizes the magnitude of optical modulation. The optical shutter device is specially designed and fabricated realizing low resistance-capacitance cell structures having small RC-time constant. The optical shutter is positioned in front of a standard high resolution CMOS image sensor and modulates the IR image reflected from the object to capture a depth image. Suggested novel optical shutter device enables capturing of a full HD depth image with depth accuracy of mm-scale, which is the largest depth image resolution among the-state-of-the-arts, which have been limited up to VGA. The 3D camera prototype realizes color/depth concurrent sensing optical architecture to capture 14Mp color and full HD depth images, simultaneously. The resulting high definition color/depth image and its capturing device have crucial impact on 3D business eco-system in IT industry especially as 3D image sensing means in the fields of 3D camera, gesture recognition, user interface, and 3D display. This paper presents MEMS-based optical shutter design, fabrication, characterization, 3D camera system prototype and image test results.

3M™ Molecular detection system versus MALDI-TOF mass spectrometry and molecular techniques for the identification of Escherichia coli 0157:H7, Salmonella spp. &Listeria spp.

PubMed

Loff, Marché; Mare, Louise; de Kwaadsteniet, Michele; Khan, Wesaal

2014-06-01

The aim of this study was to compare standard selective plating, conventional PCR (16S rRNA and species specific primers), MALDI-TOF MS and the 3M™ Molecular Detection System for the routine detection of the pathogens Listeria, Salmonella and Escherichia coli 0157:H7 in wastewater and river water samples. MALDI-TOF MS was able to positively identify 20/21 (95%) of the E. coli isolates obtained at genus and species level, while 16S rRNA sequencing only correctly identified 6/21 (28%) as E. coli strains. None of the presumptive positive Listeria spp. and Salmonella spp. isolates obtained by culturing on selective media were positively identified by MALDI-TOF and 16S rRNA analysis. The species-specific E. coli 0157:H7 PCR described in this present study, was not able to detect any E. coli 0157:H7 strains in the wastewater and river water samples analysed. However, E. coli strains, Listeria spp., L. monocytogenes and Salmonella spp. were detected using species specific PCR. Escherichia coli 0157:H7, Listeria spp. and Salmonella spp. were also sporadically detected throughout the sampling period in the wastewater and river water samples analysed by the 3M™ Molecular Detection System. MALDI-TOF MS, which is a simple, accurate and cost-effective detection method, efficiently identified the culturable organisms, while in the current study both species specific PCR (Listeria spp. and Salmonella spp.) and 3M™ Molecular Detection System could be utilised for the direct routine analysis of pathogens in water sources. Copyright © 2014 Elsevier B.V. All rights reserved.

Advantages of TOF-SIMS analysis of hydroxyapatite and fluorapatite in comparison with XRD, HR-TEM and FT-IR.

PubMed

Okazaki, Masayuki; Hirata, Isao; Matsumoto, Takuya; Takahashi, Junzo

2005-12-01

The chemical analysis of hydroxyapatite and fluorapatite was carried out using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Hydroxyapatite and fluorapatite were synthesized at 80 +/- 1 degrees C and pH 7.4 +/- 0.2. Fluorapatite was better crystallized, with its (300) reflection shifted to a slightly higher angle. High-resolution transmission electron microscopy clearly revealed a typical, regular hexagonal cross section perpendicular to the c-axis for fluorapatite and a flattened hexagonal cross section for hydroxyapatite. FT-IR spectra of fluorapatite confirmed the absence of OH absorption peak--which was seen in hydroxyapatite at about 3570 cm(-1). TOF-SIMS mass spectra showed a peak at 40 amu due to calcium. In addition, a peak at 19 amu due to fluorine could be clearly seen, although the intensities of PO, PO2, and PO3 were very low. It was confirmed that TOF-SIMS clearly showed the differences between positive and negative mass spectra of hydroxyapatite and fluorapatite, especially for F-. We concluded that TOF-SIMS exhibited distinct advantages compared with other methods of analysis.

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.

PubMed

Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry

PubMed Central

Yao, Jingwen; Utsunomiya, Shin-ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/). PMID:26819872

Proteomics analysis identified peroxiredoxin 2 involved in early-phase left ventricular impairment in hamsters with cardiomyopathy.

PubMed

Kuzuya, Kentaro; Ichihara, Sahoko; Suzuki, Yuka; Inoue, Chisa; Ichihara, Gaku; Kurimoto, Syota; Oikawa, Shinji

2018-01-01

Given the hypothesis that inflammation plays a critical role in the progression of cardiovascular diseases, the aim of the present study was to identify new diagnostic and prognostic biomarkers of myocardial proteins involved in early-phase cardiac impairment, using proteomics analysis. Using the two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) combined with MALDI-TOF/TOF tandem mass spectrometry, we compared differences in the expression of proteins in the whole left ventricles between control hamsters, dilated cardiomyopathic hamsters (TO-2), and hypertrophy cardiomyopathic hamsters (Bio14.6) at 6 weeks of age (n = 6, each group). Proteomic analysis identified 10 protein spots with significant alterations, with 7 up-regulated and 3 down-regulated proteins in the left ventricles of both TO-2 and Bio 14.6 hamsters, compared with control hamsters. Of the total alterations, peroxiredoxin 2 (PRDX2) showed significant upregulation in the left ventricles of TO-2 and Bio 14.6 hamsters. Our data suggest that PRDX2, a redox regulating molecule, is involved in early-phase left ventricular impairment in hamsters with cardiomyopathy.

[Nano-ESI-MS/MS identification on differentiation-associated proteins in M1 mouse myeloid leukemia cells induced by IL-6].

PubMed

Xia, Qing; Wang, Hong-xia; Wang, Jie; Liu, Bing-yu; Hu, Mei-ru; Zhang, Xue-min; Shen, Bei-fen

2004-10-01

To identify two differentiation-associated proteins induced by rhIL-6 in M1 mouse myeloid leukemia cells. Protein spots were excised from 2-D gels and digested in-gel with trypsin. The trypsin lysis products were first analyzed by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) through peptide mass fingerprinting and then performed peptide sequencing by nano-electrospray ionization mass spectrometry/mass spectrometry (nano-ESI-MS/MS). The database search was finished with the Mascot search engine (http://www.matrixscience.co.uk) using the data processed through MaxEnt3 and MasSeq. The two proteins were not revealed by peptide mass fingerprint using MALDI-TOF-MS, while they were respectively identified as Destrin and Putative protein after the sequence of their trypic peptides were obtained by the nano-ESI-MS/MS techniques. Nano-ESI-MS/MS technique can successfully identify the two differentiation-associated proteins induced by rhIL-6 and has great advantage in protein analysis.

Penilumamide, a novel lumazine peptide isolated from the marine-derived fungus, Penicillium sp. CNL-338†

PubMed Central

Meyer, Sven W.; Mordhorst, Thorsten F.; Lee, Choonghwan; Jensen, Paul R.; Fenical, William; Köck, Matthias

2013-01-01

A novel lumazine peptide, penilumamide (1), was isolated from the fermentation broth of a marine-derived fungal strain, identified as Penicillium sp. (strain CNL-338) and the structure of the new metabolite was determined by analysis of ESI-TOF MS data combined with 1D and 2D NMR experiments. PMID:20401392

Hydrogen/deuterium exchange, a unique and effective method for MS fragmentation behavior elucidation of ginkgolides and its application to systematic research in Ginkgo biloba.

PubMed

Niu, Xingliang; Luo, Jun; Xu, Deran; Zou, Hongyan; Kong, Lingyi

2017-02-05

Ginkgolides, the main active constituents of Ginkgo biloba, possess significant selectively inhibition on platelet-activating factor and pancreatic lipase and attract wide attention in pharmacological research area. In our study, an effective hydrogen/deuterium (H/D) exchange method was developed by exchanging the α-Hs of lactone groups in ginkgolides with Ds, which was very useful for the elucidation of the fragmentation patterns of ginkgolides in Quadrupole Time-of-flight Mass Spectrometry (Q-TOF-MS), especially in accurately distinguishing the type and position of substituent in framework of ginkgolides. Then, a systematic research strategy for qualitative and quantitative analysis of ginkgolides, based on H/D exchange, tandem solid-phase extraction and LC-Q-TOF-MS, was developed, which was successfully applied in each medicinal part of G. biloba, which indicated that ginkgolide B was the most abundant ginkgolide in the seeds of G. biloba (60.6μg/g). This research was the successful application of H/D exchange in natural products, and proved that H/D exchange is a potential method for analysis research of complex TCMs active constituents. Copyright © 2016 Elsevier B.V. All rights reserved.

The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

PubMed

Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

2016-10-05

Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.

Evaluation of meglumine gadoterate-enhanced MR angiography (MRA) compared with time-of-flight MRA in the diagnosis of clinically significant non-coronary arterial disease: a pooled analysis of data from two clinical trials

PubMed Central

Shah, D J; Lim, T-H

2012-01-01

Objectives We analysed pooled data from two clinical trials to assess the diagnostic accuracy and safety of meglumine gadoterate (Gd-DOTA)-enhanced MR angiography (MRA) relative to those of non-enhanced time-of-flight (TOF) MRA for non-coronary arterial disease. Both techniques were compared with X-ray angiography as the gold standard. Methods Patients were of both sexes, were aged at least 18 years and had suspected non-coronary arterial disease. Each patient was his/her own control and underwent TOF MRA followed by Gd-DOTA-enhanced MRA, and then X-ray angiography. MRA was performed at 1.5 T (USA study) or 3 T (Republic of Korea study). The primary criterion used to evaluate efficacy was the degree to which the MRA examination agreed with X-ray angiography in assessing non-coronary arterial lesions. The performance of Gd-DOTA over TOF was assessed using a one-sided paired t-test. We also evaluated the specificity, sensitivity, image quality, examination duration and clinical safety of both MRA procedures. Results In total, 192 patients were enrolled and received Gd-DOTA. In the intent-to-treat population (n=162), within-patient accuracy was significantly greater for Gd-DOTA than for TOF (85.8±19.8% agreement between Gd-DOTA and X-ray angiography compared with 78.3±24.9% agreement between TOF and X-ray angiography; p=0.0001). The sensitivity, specificity, image quality and examination duration were also better for Gd-DOTA than for TOF. There were no serious drug-related adverse events. Conclusion We conclude that Gd-DOTA-enhanced MRA is a safe and accurate procedure for detecting arterial stenosis at both 1.5 T and 3 T. PMID:22167518

Antioxidant, genotoxic and antigenotoxic activities of daphne gnidium leaf extracts

PubMed Central

2012-01-01

Background Plants play a significant role in maintaining human health and improving the quality of human life. They serve humans well as valuable components of food, as well as in cosmetics, dyes, and medicines. In fact, many plant extracts prepared from plants have been shown to exert biological activity in vitro and in vivo. The present study explored antioxidant and antigenotoxic effects of Daphne gnidium leaf extracts. Methods The genotoxic potential of petroleum ether, chloroform, ethyl acetate, methanol and total oligomer flavonoid (TOF) enriched extracts from leaves of Daphne gnidium, was assessed using Escherichia coli PQ37. Likewise, the antigenotoxicity of the same extracts was tested using the “SOS chromotest test”. Antioxidant activities were studied using non enzymatic and enzymatic method: NBT/Riboflavine and xantine oxidase. Results None of the different extracts produced a genotoxic effect, except TOF extract at the lowest tested dose. Our results showed that D. gnidium leaf extracts possess an antigenotoxic effect against the nitrofurantoin a mutagen of reference. Ethyl acetate and TOF extracts were the most effective in inhibiting xanthine oxidase activity. While, methanol extract was the most potent superoxide scavenger when tested with the NBT/Riboflavine assay. Conclusions The present study has demonstrated that D. gnidium leaf extract possess antioxidant and antigenotoxic effects. These activities could be ascribed to compounds like polyphenols and flavonoid. Further studies are required to isolate the active molecules. PMID:22974481

3D imaging LADAR with linear array devices: laser, detector and ROIC

NASA Astrophysics Data System (ADS)

Kameyama, Shumpei; Imaki, Masaharu; Tamagawa, Yasuhisa; Akino, Yosuke; Hirai, Akihito; Ishimura, Eitaro; Hirano, Yoshihito

2009-07-01

This paper introduces the recent development of 3D imaging LADAR (LAser Detection And Ranging) in Mitsubishi Electric Corporation. The system consists of in-house-made key devices which are linear array: the laser, the detector and the ROIC (Read-Out Integrated Circuit). The laser transmitter is the high power and compact planar waveguide array laser at the wavelength of 1.5 micron. The detector array consists of the low excess noise Avalanche Photo Diode (APD) using the InAlAs multiplication layer. The analog ROIC array, which is fabricated in the SiGe- BiCMOS process, includes the Trans-Impedance Amplifiers (TIA), the peak intensity detectors, the Time-Of-Flight (TOF) detectors, and the multiplexers for read-out. This device has the feature in its detection ability for the small signal by optimizing the peak intensity detection circuit. By combining these devices with the one dimensional fast scanner, the real-time 3D range image can be obtained. After the explanations about the key devices, some 3D imaging results are demonstrated using the single element key devices. The imaging using the developed array devices is planned in the near future.

Syringic Acid Extracted from Herba dendrobii Prevents Diabetic Cataract Pathogenesis by Inhibiting Aldose Reductase Activity

PubMed Central

Wei, Xiaoyong; Chen, Dan; Yi, Yanchun; Qi, Hui; Gao, Xinxin; Fang, Hua; Gu, Qiong; Wang, Ling; Gu, Lianquan

2012-01-01

Objective. Effects of Syringic acid (SA) extracted from dendrobii on diabetic cataract (DC) pathogenesis were explored. Methods. Both in vitro and in vivo DC lens models were established using D-gal, and proliferation of HLEC exposed to SA was determined by MMT assay. After 60-day treatment with SA, rat lens transparency was observed by anatomical microscopy using a slit lamp. SA protein targets were extracted and isolated using 2-DE and MALDI TOF/TOF. AR gene expression was investigated using qRT-PCR. Interaction sites and binding characteristics were determined by molecule-docking techniques and dynamic models. Results. Targeting AR, SA provided protection from D-gal-induced damage by consistently maintaining lens transparency and delaying lens turbidity development. Inhibition of AR gene expression by SA was confirmed by qRT-PCR. IC50 of SA for inhibition of AR activity was 213.17 μg/mL. AR-SA binding sites were Trp111, His110, Tyr48, Trp20, Trp79, Leu300, and Phe122. The main binding modes involved hydrophobic interactions and hydrogen bonding. The stoichiometric ratio of non-covalent bonding between SA and AR was 1.0 to 13.3. Conclusion. SA acts to prevent DC in rat lenses by inhibiting AR activity and gene expression, which has potential to be developed into a novel drug for therapeutic management of DC. PMID:23365598

[Value of MR imaging and MR angiography in the differential diagnosis of carotid space tumour].

PubMed

Liu, Pei-fang; Li, Xin; Bao, Run-xian; Liu, Jing-zu; Ge, Zheng-jin

2004-04-01

To determine the imaging features of magnetic resonance imaging (MRI) and 2D time of flight (TOF) MR angiography (MRA) and study the value in the differential diagnosis and surgical planning for carotid space tumors. Twenty-six patients with suspected pulsatile carotid space mass were imaged by MRI and 2D TOF MRA from 1996 to 2003. Its characteristic findings were analyzed for lesion shape, margin, signal intensity, angle of common carotid bifurcation, and the relationship between the great vessels and carotid space mass. Of the 26 patients, 22 were verified histopathologically, including 15 carotid body tumors (1 patient had bilateral carotid body tumors), 4 carotid artery aneurysms, 3 schwannomas, and 1 metastatic carcinoma. The rest four patients had clinical pseudomasses proved by MRI and MRA as considerable dilated or tortuous carotid artery as compared with the contralateral one. Combined MRI and MRA assessment of carotid body tumors and carotid artery aneurysm yielded an accuracy of 100%. It was also revealed that the anatomy shown on the MRI and axial MRA source images was consistent with that found by surgery. MRI in combination with MRA is considered as non-invasive imaging technique for the evaluation of carotid space tumor showing superiority to other modalities in the differential diagnosis between vascular versus non-vascular tumours. This method may take the place of traumatic carotid angiography.

The use of Gram stain and matrix-assisted laser desorption ionization time-of-flight mass spectrometry on positive blood culture: synergy between new and old technology.

PubMed

Fuglsang-Damgaard, David; Nielsen, Camilla Houlberg; Mandrup, Elisabeth; Fuursted, Kurt

2011-10-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is promising as an alternative to more costly and cumbersome methods for direct identifications in blood cultures. We wanted to evaluate a simplified pre-treatment method for using MALDI-TOF-MS directly on positive blood cultures using BacT/Alert blood culture system, and to test an algorithm combining the result of the initial microscopy with the result suggested by MALDI-TOF-MS. Using the recommended cut-off score of 1.7 the best results were obtained among Gram-negative rods with correct identifications in 91% of Enterobacteriaceae, 83% in aerobic/non-fermentative Gram-negative rods, whereas results were more modest among Gram-positive cocci with correct identifications in 52% of Staphylococci, 54% in Enterococci and only 20% in Streptococci. Combining the results of Gram stain with the top reports by MALDI-TOF-MS, increased the sensitivity from 91% to 93% in the score range from 1.5 to 1.7 and from 48% to 85% in the score range from 1.3 to 1.5. Thus, using this strategy and accepting a cut-off at 1.3 instead of the suggested 1.7, overall sensitivity could be increased from 88.1% to 96.3%. MALDI-TOF-MS is an efficient method for direct routine identification of bacterial isolates in blood culture, especially when combined with the result of the Gram stain. © 2011 The Authors. APMIS © 2011 APMIS.

Study of carrier-mobility of organic thin film by dark-injection time-of-flight and electric-field-induced optical second-harmonic generation measurements

NASA Astrophysics Data System (ADS)

Li, Xin; Sunaga, Masashi; Taguchi, Dai; Manaka, Takaaki; Lin, Hong; Iwamoto, Mitsumasa

2017-06-01

By using dark-injection time-of-flight (ToF) and time-resolved electric-field-induced optical second-harmonic generation (EFISHG) measurements, we studied carrier mobility μ of pentacene (Pen) thin film of ITO/Pen/Al and Au/Pen/polyimide/ITO diodes where pentacene film is ∼100 nm in thickness. ToF showed that determination of transit time tr from trace of transient currents is difficult owing to large capacitive charging current. On the other hand, optical EFISHG is free from this charging current, and allows us to calculate hole and electron mobility as μh = 1.8 ×10-4 cm2/Vs and μe = 7.6 ×10-7 cm2/Vs, respectively, by using the relation tr = d / μ ∫tc tr E (0) dt (d : Pen thickness, E (0) : electric field across Pen), instead of the conventional relationship tr =d2 / μV (V : voltage across Pen). Time-resolved EFISHG measurement is useful for the determination of carrier mobility of organic thin film in organic devices.

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation.

PubMed

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-07

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical FDG-PET study also revealed that for the same noise level, a higher contrast recovery can be obtained by increasing the number of TOF subsets. It can be concluded that the proposed TOF weighting matrix pre-computation and subsetization approaches enable to further accelerate and improve the convergence properties of OSEM and MLEM algorithms, thus opening new avenues for accelerated TOF PET image reconstruction.

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation

NASA Astrophysics Data System (ADS)

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-01

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical FDG-PET study also revealed that for the same noise level, a higher contrast recovery can be obtained by increasing the number of TOF subsets. It can be concluded that the proposed TOF weighting matrix pre-computation and subsetization approaches enable to further accelerate and improve the convergence properties of OSEM and MLEM algorithms, thus opening new avenues for accelerated TOF PET image reconstruction.

Effects of right ventricular hemodynamic burden on intraventricular flow in tetralogy of fallot: an echocardiographic contrast particle imaging velocimetry study.

PubMed

Kutty, Shelby; Li, Ling; Danford, David A; Houle, Helene; Datta, Saurabh; Mancina, Joel; Xiao, Yunbin; Pedrizzetti, Gianni; Porter, Thomas R

2014-12-01

The purpose of this investigation was to test the hypothesis that flow patterns in the right ventricle are abnormal in patients with repaired tetralogy of Fallot (TOF). High-resolution echocardiographic contrast particle imaging velocimetry was used to investigate rotation intensity and kinetic energy dissipation of right ventricular (RV) flow in patients with TOF compared with normal controls. Forty-one subjects (16 with repaired TOF and varying degrees of RV dilation and 25 normal controls) underwent prospective contrast imaging using the lipid-encapsulated microbubble (Definity) on Sequoia systems. A mechanical index of 0.4, three-beat high-frame rate (>60 Hz) captures, and harmonic frequencies were used. Rotation intensity and kinetic energy dissipation of flow in the right and left ventricles were studied (Hyperflow). Ventricular volumes and ejection fractions in all subjects were derived from same-day cardiac magnetic resonance (CMR). Measurable planar maps were obtained for the left ventricle in 14 patients and the right ventricle in 10 patients among those with TOF and for the left ventricle in 23 controls and the right ventricle in 21 controls. Compared with controls, the TOF group had higher RV indexed end-diastolic volumes (117.8 ± 25.5 vs 88 ± 15.4 mL/m(2), P < .001) and lower RV ejection fractions (44.6 ± 3.6% vs 51.8 ± 3.6%, P < .001). Steady-streaming (heartbeat-averaged) flow rotation intensities were higher in patients with TOF for the left ventricle (0.4 ± 0.13 vs 0.29 ± 0.08, P = .012) and the right ventricle (0.53 ± 0.15 vs 0.26 ± 0.12, P < .001), whereas kinetic energy dissipation in TOF ventricles was lower (for the left ventricle, 0.51 ± 0.29 vs 1.52 ± 0.69, P < .001; for the right ventricle, 0.4 ± 0.24 vs 1.65 ± 0.91, P < .001). It is feasible to characterize RV and left ventricular flow parameters and planar maps in adolescents and adults with repaired TOF using echocardiographic contrast particle imaging velocimetry. Intraventricular flow patterns in the abnormal and/or enlarged right ventricle in patients with TOF differ from those in normal young adults. The rotation intensity and energy dissipation trends in this investigation suggest that they may be quantitative markers of RV and left ventricular compliance abnormalities in patients with repaired TOF. This hypothesis merits further investigation. Copyright © 2014 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Relationship between the UPLC-Q-TOF-MS fingerprinted constituents from Daphne genkwa and their anti-inflammatory, anti-oxidant activities.

PubMed

Du, Wen-Juan; Ji, Jun; Wang, Ling; Lan, Xin-Yi; Li, Jia; Lei, Jun-Qiu; He, Xin; Zhang, Chun-Feng; Huang, Wen-Zhe; Wang, Zhen-Zhong; Xiao, Wei; Wang, Chong-Zhi; Yuan, Chun-Su

2017-12-01

Daphne genkwa Sieb.et Zucc. is a well-known medicinal plant. This study was designed to apply the ultra-high performance liquid chromatography system to establish a quality control method for D. genkwa. Data revealed that there were 15 common peaks in 10 batches of D. genkwa Sieb. Et Zucc. (Thymelaeaceae) from different provinces of China. On this basis, the fingerprint chromatogram was established to provide references for quality control. Afterwards, the chemical constitutions of these common peaks were analyzed using the UPLC-Q-TOF-MS system and nine of them were identified. In addition, LPS-stimulated RAW264.7 murine macrophages and DPPH assay were used to study the anti-inflammatory and anti-oxidation effects of D. genkwa. Then the fingerprint-efficacy relationships between UPLC fingerprints and pharmacodynamic data were studied with canonical correlation analysis. Analysis results indicated that the anti-inflammatory and anti-oxidation effects differed among the 10 D. genkwa samples owing to their inherent differences of chemical compositions. Taken together, this research established a fingerprint-efficacy relationship model of D. genkwa plant by combining the UPLC analytic technique and pharmacological research, which provided references for the detection of the principal components of traditional Chinese medicine on bioactivity. Copyright © 2017 John Wiley & Sons, Ltd.

Three-dimensional tracking and imaging laser scanner for space operations

NASA Astrophysics Data System (ADS)

Laurin, Denis G.; Beraldin, J. A.; Blais, Francois; Rioux, Marc; Cournoyer, Luc

1999-05-01

This paper presents the development of a laser range scanner (LARS) as a three-dimensional sensor for space applications. The scanner is a versatile system capable of doing surface imaging, target ranging and tracking. It is capable of short range (0.5 m to 20 m) and long range (20 m to 10 km) sensing using triangulation and time-of-flight (TOF) methods respectively. At short range (1 m), the resolution is sub-millimeter and drops gradually with distance (2 cm at 10 m). For long range, the TOF provides a constant resolution of plus or minus 3 cm, independent of range. The LARS could complement the existing Canadian Space Vision System (CSVS) for robotic manipulation. As an active vision system, the LARS is immune to sunlight and adverse lighting; this is a major advantage over the CSVS, as outlined in this paper. The LARS could also replace existing radar systems used for rendezvous and docking. There are clear advantages of an optical system over a microwave radar in terms of size, mass, power and precision. Equipped with two high-speed galvanometers, the laser can be steered to address any point in a 30 degree X 30 degree field of view. The scanning can be continuous (raster scan, Lissajous) or direct (random). This gives the scanner the ability to register high-resolution 3D images of range and intensity (up to 4000 X 4000 pixels) and to perform point target tracking as well as object recognition and geometrical tracking. The imaging capability of the scanner using an eye-safe laser is demonstrated. An efficient fiber laser delivers 60 mW of CW or 3 (mu) J pulses at 20 kHz for TOF operation. Implementation of search and track of multiple targets is also demonstrated. For a single target, refresh rates up to 137 Hz is possible. Considerations for space qualification of the scanner are discussed. Typical space operations, such as docking, object attitude tracking, and inspections are described.

Biotransformation and metabolic profile of caudatin-2,6-dideoxy-3-O-methy-β-d-cymaropyranoside with human intestinal microflora by liquid chromatography quadrupole time-of-flight mass spectrometry.

PubMed

Zhang, Wei; Peng, Yun-ru; Ding, Yong-fang

2015-11-01

In our previous studies, caudatin-2,6-dideoxy-3-O-methy-β-d- cymaropyranoside (CDMC) was for the first time isolated from Cynanchum auriculatum Royle ex Wightand and was reported to possess a wide range of biological activities. However, the routes and metabolites of CDMC produced by intestinal bacteria are not well understood. In this study, ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) technique combined with Metabolynx(TM) software was applied to analyze metabolites of CDMC by human intestinal bacteria. The incubated samples collected for 48 h in an anaerobic incubator and extracted with ethyl acetate were analyzed by UPLC-Q-TOF-MS within 12 min. Eight metabolites were identified based on MS and MS/MS data. The results indicated that hydrolysis, hydrogenation, demethylation and hydroxylation were the major metabolic pathways of CDMC in vitro. Seven strains of bacteria including Bacillus sp. 46, Enterococcus sp. 30 and sp. 45, Escherichia sp. 49A, sp. 64, sp. 68 and sp. 75 were further identified using 16S rRNA gene sequencing owing to their relatively strong metabolic capacity toward CDMC. The present study provides important information about metabolic routes of CDMC and the roles of different intestinal bacteria in the metabolism of CDMC. Moreover, those metabolites might influence the biological effect of CDMC in vivo, which affects the clinical effects of this medicinal plant. Copyright © 2015 John Wiley & Sons, Ltd.

Top-down proteomic identification of bacterial protein biomarkers and toxins using MALDI-TOF-TOF-MS/MS and post-source decay

USDA-ARS?s Scientific Manuscript database

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry(MALDI-TOF-TOF-MS)has provided new capabilities for the rapid identification of digested and non-digested proteins. The tandem (MS/MS) capability of TOF-TOF instruments allows precursor ion selection/isolation...

[Separation and identification of bovine lactoferricin by high performance liquid chromatography-matrix-assisted laser desorption/ionization time of flight/ time of flight mass spectrometry].

PubMed

An, Meichen; Liu, Ning

2010-02-01

A high performance liquid chromatography-matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometry (HPLC-MALDI-TOF/TOF MS) method was developed for the separation and identification of bovine lactoferricin (LfcinB). Bovine lactoferrin was hydrolyzed by pepsin and then separated by ion exchange chromatography and reversed-phase liquid chromatography (RP-LC). The antibacterial activities of the fractions from RP-LC separation were determined and the protein concentration of the fraction with the highest activity was measured, whose sequence was indentified by MALDI-TOF/TOF MS. The relative molecular mass of LfcinB was 3 124.89 and the protein concentration was 18.20 microg/mL. The method of producing LfcinB proposed in this study has fast speed, high accuracy and high resolution.

Evaluation of Three MALDI-TOF Mass Spectrometry Libraries for the Identification of Filamentous Fungi in Three Clinical Microbiology Laboratories in Manitoba, Canada.

PubMed

Stein, Markus; Tran, Vanessa; Nichol, Kimberly A; Lagacé-Wiens, Philippe; Pieroni, Peter; Adam, Heather J; Turenne, Christine; Walkty, Andrew J; Normand, Anne-Cécile; Hendrickx, Marijke; Piarroux, Renaud; Karlowsky, James A

2018-06-12

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify bacterial pathogens and yeasts, but not for the identification of moulds. Recent progress in extraction protocols and the composition of comparative libraries support potential application of MALDI-TOF MS for mould identification in clinical microbiology laboratories. We evaluated the performance of the Bruker Microflex ™ MALDI-TOF MS instrument (Billerica, MA, USA) to identify clinical isolates and reference strains of moulds using three libraries, the Bruker mould library, the National Institutes of Health (NIH) library, and the Mass Spectrometry Identification (MSI) online library, and compared those results to conventional (morphological) and molecular (18S/ITS; gold standard) identification methods. All three libraries demonstrated greater accuracy in genus identification (≥94.9%) than conventional methods (86.4%). MALDI-TOF MS identified 73.3% of isolates to species-level compared to only 31.7% by conventional methods. The MSI library demonstrated the highest rate of species-level identification (72.0%) compared to NIH (19.5%) and Bruker (13.6%) libraries. Greater than 20% of moulds remained unidentified to species-level by all three MALDI-TOF MS libraries primarily because of library limitations or imperfect spectra. The overall identification rate of each MALDI-TOF MS library depended on the number of species and the number of spectra representing each species in the library. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Landslide Spreading, Impulse Water Waves and Modelling of the Vajont Rockslide

NASA Astrophysics Data System (ADS)

Crosta, Giovanni B.; Imposimato, Silvia; Roddeman, Dennis

2016-06-01

Landslides can occur in different environments and can interact with or fall into water reservoirs or open sea with different characteristics. The subaerial evolution and the transition from subaerial to subaqueous conditions can strongly control the landslide evolution and the generated impulse waves, and consequently the final hazard zonation. We intend to model the landslide spreading, the impact with the water surface and the generation of the impulse wave under different 2D and 3D conditions and settings. We verify the capabilities of a fully 2D and 3D FEM ALE approach to model and analyse near-field evolution. To this aim we validate the code against 2D laboratory experiments for different Froude number conditions (Fr = 1.4, 3.2). Then the Vajont rockslide (Fr = 0.26-0.75) and the consequent impulse wave are simulated in 2D and 3D. The sliding mass is simulated as an elasto-plastic Mohr-Coulomb material and the lake water as a fully inviscid low compressibility fluid. The rockslide model is validated against field observations, including the total duration, the profile and internal geometry of the final deposit, the maximum water run-up on the opposite valley flank and on the rockslide mass. 2D models are presented for both the case of a dry valley and that of the impounded lake. The set of fully 3D simulations are the first ones available and considering the rockslide evolution, propagation and interaction with the water reservoir. Advantages and disadvantages of the modelling approach are discussed.

Generating 3D and 3D-like animations of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs.

PubMed

Hortolà, Policarp

2010-01-01

When dealing with microscopic still images of some kinds of samples, the out-of-focus problem represents a particularly serious limiting factor for the subsequent generation of fully sharp 3D animations. In order to produce fully-focused 3D animations of strongly uneven surface microareas, a vertical stack of six digital secondary-electron SEM micrographs of a human bloodstain microarea was acquired. Afterwards, single combined images were generated using a macrophotography and light microscope image post-processing software. Subsequently, 3D animations of texture and topography were obtained in different formats using a combination of software tools. Finally, a 3D-like animation of a texture-topography composite was obtained in different formats using another combination of software tools. By one hand, results indicate that the use of image post-processing software not concerned primarily with electron micrographs allows to obtain, in an easy way, fully-focused images of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs. On the other hand, results also indicate that such small series of electron micrographs can be utilized for generating 3D and 3D-like animations that can subsequently be converted into different formats, by using certain user-friendly software facilities not originally designed for use in SEM, that are easily available from Internet. Although the focus of this study was on bloodstains, the methods used in it well probably are also of relevance for studying the surface microstructures of other organic or inorganic materials whose sharp displaying is difficult of obtaining from a single SEM micrograph.

Implications for Extraterrestrial Hydrocarbon Chemistry: Analysis of Ethylene (C{sub 2}H{sub 4}) and D4-Ethylene (C{sub 2}D{sub 4}) Ices Exposed to Ionizing Radiation via Combined Infrared Spectroscopy and Reflectron Time-of-flight Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abplanalp, Matthew J.; Kaiser, Ralf I., E-mail: ra

The processing of the hydrocarbon ice, ethylene (C{sub 2}H{sub 4}/C{sub 2}D{sub 4}), via energetic electrons, thus simulating the processes in the track of galactic cosmic-ray particles, was carried out in an ultrahigh vacuum apparatus. The chemical evolution of the ices was monitored online and in situ utilizing Fourier transform infrared spectroscopy (FTIR) and during temperature programmed desorption, via a quadrupole mass spectrometer utilizing electron impact ionization (EI-QMS) and a reflectron time-of-flight mass spectrometer utilizing a photoionization source (PI-ReTOF-MS). Several previous in situ studies of ethylene ice irradiation using FTIR were substantiated with the detection of six products: [CH{sub 4} (CD{submore » 4})], acetylene [C{sub 2}H{sub 2} (C{sub 2}D{sub 2})], the ethyl radical [C{sub 2}H{sub 5} (C{sub 2}D{sub 5})], ethane [C{sub 2}H{sub 6} (C{sub 2}D{sub 6})], 1-butene [C{sub 4}H{sub 8} (C{sub 4}D{sub 8})], and n -butane [C{sub 4}H{sub 10} (C{sub 4}D{sub 10})]. Contrary to previous gas phase studies, the PI-ReTOF-MS detected several groups of hydrocarbon with varying degrees of saturation: C{sub n}H{sub 2n+2} (n = 4–10), C{sub n}H{sub 2n} ( n = 2–12, 14, 16), C{sub n}H{sub 2n−2} ( n = 3–12, 14, 16), C{sub n}H{sub 2n−4} (n = 4–12, 14, 16), C{sub n}H{sub 2n−6} (n = 4–10, 12), C{sub n}H{sub 2n−8} ( n = 6–10), and C{sub n}H{sub 2n−10} ( n = 6–10). Multiple laboratory studies have shown the facile production of ethylene from methane, which is a known ice constituent in the interstellar medium. Various astrophysically interesting molecules can be associated with the groups detected here, such as allene/methylacetylene (C{sub 3}H{sub 4}) or 1, 3-butadiene (C{sub 4}H{sub 6}) and its isomers, which have been shown to lead to polycyclic aromatic hydrocarbons. Finally, several hydrocarbon groups detected here are unique to ethylene ice versus ethane ice and may provide understanding of how complex hydrocarbons form in astrophysical environments.« less

3D modeling based on CityEngine

NASA Astrophysics Data System (ADS)

Jia, Guangyin; Liao, Kaiju

2017-03-01

Currently, there are many 3D modeling softwares, like 3DMAX, AUTOCAD, and more populous BIM softwares represented by REVIT. CityEngine modeling software introduced in this paper can fully utilize the existing GIS data and combine other built models to make 3D modeling on internal and external part of buildings in a rapid and batch manner, so as to improve the 3D modeling efficiency.

Cerebral TOF Angiography at 7T: Impact of B1+ Shimming with a 16-Channel Transceiver Array

PubMed Central

Schmitter, Sebastian; Wu, Xiaoping; Adriany, Gregor; Auerbach, Edward J.; Uğurbil, Kâmil; Van de Moortele, Pierre-François

2014-01-01

Purpose Time-of-flight (TOF) MR imaging is clinically among the most common cerebral non-contrast enhanced MR angiography techniques allowing for high spatial resolution. As shown by several groups TOF contrast significantly improves at ultra-high field (UHF) of B0=7T, however, spatially varying transmit B1 (B1+) fields at 7T reduce TOF contrast uniformity, typically resulting in sub-optimal contrast and reduced vessel conspicuity in the brain periphery. Methods Using a 16-channel B1+ shimming system we compare different dynamically applied B1+ phase shimming approaches on the RF excitation to improve contrast homogeneity for a (0.5 mm)3 resolution multi-slab TOF acquisition. In addition, B1+ shimming applied on the venous saturation pulse was investigated to improve venous suppression, subcutaneous fat signal reduction and enhanced background suppression originating from MT effect. Results B1+ excitation homogeneity was improved by a factor 2.2 to 2.6 on average depending on the shimming approach, compared to a standard CP-like phase setting, leading to improved vessel conspicuity particularly in the periphery. Stronger saturation, higher fat suppression and improved background suppression were observed when dynamically applying B1+ shimming on the venous saturation pulse. Conclusion B1+ shimming can significantly improve high resolution TOF vascular investigations at UHF, holding strong promise for non contrast-enhanced clinical applications. PMID:23640915

Integrative proteome analysis of Brachypodium distachyon roots and leaves reveals a synergetic responsive network under H2O2 stress.

PubMed

Bian, Yan-Wei; Lv, Dong-Wen; Cheng, Zhi-Wei; Gu, Ai-Qin; Cao, Hui; Yan, Yue-Ming

2015-10-14

The plant oxidative stress response is vital for defense against various abiotic and biotic stresses. In this study, ultrastructural changes and the proteomic response to H2O2 stress in roots and leaves of the model plant Brachypodium distachyon were studied. Transmission electron microscopy (TEM) showed that the ultrastructural damage in roots was more serious than in leaves. Particularly, the ultrastructures of organelles and the nucleus in root tip cells were damaged, leading to the inhibition of normal biological activities of roots, which then spread throughout the plant. Based on two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF-MS, 84 and 53 differentially accumulated protein (DAP) spots representing 75 and 45 unique proteins responsive to H2O2 stress in roots and leaves, respectively, were identified. These protein species were mainly involved in signal transduction, energy metabolism, redox homeostasis/stress defense, protein folding/degradation, and cell wall/cell structure. Interestingly, two 14-3-3 proteins (GF14-B and GF14-D) were identified as DAPs in both roots and leaves. Protein-protein interaction (PPI) analysis revealed a synergetic H2O2-responsive network. Copyright © 2015 Elsevier B.V. All rights reserved.

The MIT HEDP Accelerator Facility for education and advanced diagnostics development for OMEGA, Z and the NIF

NASA Astrophysics Data System (ADS)

Petrasso, R.; Gatu Johnson, M.; Armstrong, E.; Han, H. W.; Kabadi, N.; Lahmann, B.; Orozco, D.; Rojas Herrera, J.; Sio, H.; Sutcliffe, G.; Frenje, J.; Li, C. K.; Séguin, F. H.; Leeper, R.; Ruiz, C. L.; Sangster, T. C.

2015-11-01

The MIT HEDP Accelerator Facility utilizes a 135-keV linear electrostatic ion accelerator, a D-T neutron source and two x-ray sources for development and characterization of nuclear diagnostics for OMEGA, Z, and the NIF. The ion accelerator generates D-D and D-3He fusion products through acceleration of D ions onto a 3He-doped Erbium-Deuteride target. Fusion reaction rates around 106 s-1 are routinely achieved, and fluence and energy of the fusion products have been accurately characterized. The D-T neutron source generates up to 6 × 108 neutrons/s. The two x-ray generators produce spectra with peak energies of 35 keV and 225 keV and maximum dose rates of 0.5 Gy/min and 12 Gy/min, respectively. Diagnostics developed and calibrated at this facility include CR-39 based charged-particle spectrometers, neutron detectors, and the particle Time-Of-Flight (pTOF) and Magnetic PTOF CVD-diamond-based bang time detectors. The accelerator is also a vital tool in the education of graduate and undergraduate students at MIT. This work was supported in part by SNL, DOE, LLE and LLNL.

Therapeutic Targeting of P2X7 after TBI

DTIC Science & Technology

2012-11-16

evacuation of acute subdural hematoma : brain shift and the dynamics of extraaxial collections. Neurol Res, 26(7), 763-766. Cold, G. E., & Jensen, F. T...of consecutive bilateral surgeries for patients with acute 31 Kimbler, Donald E N10-P10 subdural hematoma who develop contralateral acute epi...or subdural hematoma . Surg Neurol, 60(1), 23-30; discussion 30. Miller, J. D., Becker, D. P., Ward, J. D., Sullivan, H. G., Adams, W. E., & Rosner, M

Comparison of 7T and 3T MRI in patients with moyamoya disease.

PubMed

Oh, Byeong Ho; Moon, Hyeong Cheol; Baek, Hyeon Man; Lee, Youn Joo; Kim, Sang Woo; Jeon, Young Jai; Lee, Gun Seok; Kim, Hong Rae; Choi, Jai Ho; Min, Kyung Soo; Lee, Mou Seop; Kim, Young Gyu; Kim, Dong Ho; Kim, Won Seop; Park, Young Seok

2017-04-01

Magnetic resonance imaging and magnetic resonance angiography (MRI/MRA) are widely used for evaluating the moyamoya disease (MMD). This study compared the diagnostic accuracy of 7Tesla (T) and 3T MRI/MRA in MMD. In this case control study, 12 patients [median age: 34years; range (10-66years)] with MMD and 12 healthy controls [median age: 25years; range (22-59years)] underwent both 7T and 3T MRI/MRA. To evaluate the accuracy of MRI/MRA in MMD, five criteria were compared between imaging systems of 7T and 3T: Suzuki grading system, internal carotid artery (ICA) diameter, ivy sign, flow void of the basal ganglia on T2-weighted images, and high signal intensity areas of the basal ganglia on time-of-flight (TOF) source images. No difference was observed between 7T and 3T MRI/MRA in Suzuki stage, ICA diameter, and ivy sign score; while, 7T MRI/MRA showed a higher detection rate in the flow void on T2-weighted images and TOF source images (p<0.001). Receiver operating characteristic curves of both T2 and TOF criteria showed that 7T MRI/MRA had higher sensitivity and specificity than 3T MRI/MRA. Our findings indicate that 7T MRI/MRA is superior to 3T MRI/MRA for the diagnosis of MMD in point of detecting the flow void in basal ganglia by T2-weighted and TOF images. Copyright © 2016. Published by Elsevier Inc.

Ab initio determination of geometries and vibrational characteristics of building blocks of organic super-conductors: TTF and its derivatives.

PubMed

Rani, P; Yadav, R A

2012-12-01

Molecular behavior of the building block {[2-(1,3-dithiole-2-ylidene)-1,3-dithiole] ≡ tetrathiafulvalene (TTF)} of organic superconductors have been investigated along with its three derivatives, namely, {[2-(1,3-dioxole-2-ylidene)-1,3-dioxole] ≡ tetraoxafulvalene (TOF)}; [2,2]-bi -[[1,3] oxathiolylidene] ≡ Der I and 2-(3H-Furan-2-ylidene)-[1,3] oxathiole ≡ Der II. The properties of the molecules such as molecular geometries, frontier MOs and vibrational spectra have been investigated by using DFT method at the B3LYP level employing 6-311++G(d,p) basis set. The geometrical parameters and atomic charges on various atomic sites of the TTF, TOF, Ders I and II suggest extended conjugation in these systems. The present calculations lead to the reassignments for of some of the fundamentals and new interpretations for some of the observed IR and Raman frequencies. One of the two modes involved in the Fermi resonance giving rise to the doublet 1555 and 1564 cm(-1) needed to be revised and another doublet 3083 and 3108 cm(-1) could be interpreted as a Fermi resonance doublet. Out of the two ν(C = C) modes under the a(1) species, the lower frequency mode is assigned to the ν(C = C) of the ring and the higher one to the ν(C = C) of the central C = C bond contrary to the assignment reported in literature. The conducting properties of these molecules depend mainly on this mode. Copyright © 2012 Elsevier B.V. All rights reserved.

Numerical study of the 3-D effect on FEL performance and its application to the APS LEUTL FEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chae, Y.C.

A Low-Energy Undulator Test Line (LEUTL) is under construction at the Advanced Photon Source (APS). In LEUTL periodic focusing is provided by external quadrupoles. This results in an elliptical beam with its betatron oscillation envelope varying along the undulators. The free-electron laser (FEL) interaction with such a beam will exhibit truly 3-D effects. Thus the investigation of 3-D effects is important in optimizing the FEL performance. The programs GINGER and TDA3D, coupled with theoretically known facts, have been used for this purpose. Both programs are fully 3-D in moving the particle, but model the interaction between particles and axially symmetricmore » electromagnetic waves. Even though TDA3D can include a few azimuthal modes in the interaction, it is still not a fully 3-D FEL code. However, they show that these 2-D programs can still be used for an elliptical beam whose aspect ratio is within certain limits. The author presents numerical results of FEL performance for the circular beam, the elliptical beam, and finally for the beam in the realistic LEUTL lattice.« less

Mixed-Substituent Cyclophosphazenes with Calamitic and Polycatenar Mesogens.

PubMed

Jiménez, J; Callizo, L; Serrano, J L; Barberá, J; Oriol, L

2017-07-17

A synthetic strategy has been developed to prepare liquid crystalline cyclotriphosphazenes that have two different types of mesogenic units linked to the same phosphorus atom. Hexachlorocyclotriphosphazene, N 3 P 3 Cl 6 , was reacted with 3 mol of the calamitic unit 4-cyano-4'-hydroxybiphenyl to give a mixture of compounds in which the nongem-trans-trisubstituted derivative N 3 P 3 Cl 3 (OC 6 H 4 C 6 H 4 {CN}-p) 3 was the major product. The substitution of all three chlorine atoms in this nongeminal compound gave rise to the hydroxyl-functional phosphazenes, nongem-trans-N 3 P 3 (OC 6 H 4 C 6 H 4 {CN}-p) 3 (OC 6 H 4 {OH}-p) 3 or nongem-trans-N 3 P 3 (OC 6 H 4 C 6 H 4 {CH 3 }-p) 3 (OC 6 H 4 {OH}-p) 3 , from which the second mesogenic unit, a polycatenar one, was introduced. The chemical structure of the resulting materials, deduced from spectroscopic and MALDI-TOF techniques, was in accordance with monodisperse, fully functionalized cyclotriphosphazenes. Mesomorphism is highly dependent on the terminal group of the calamitic units, and liquid crystal phases were only detected on the cyano-derivatives. The calamitic or columnar nature of the mesophase depends on the number of alkyl chains of the polycatenar moieties.

Identification of cross-reactive B-cell epitopes between Bos d 9.0101(Bos Taurus) and Gly m 5.0101 (Glycine max) by epitope mapping MALDI-TOF MS.

PubMed

Candreva, Ángela María; Ferrer-Navarro, Mario; Bronsoms, Silvia; Quiroga, Alejandra; Curciarello, Renata; Cauerhff, Ana; Petruccelli, Silvana; Docena, Guillermo Horacio; Trejo, Sebastián Alejandro

2017-08-01

Exposure to cow's milk constitutes one of the most common causes of food allergy. In addition, exposure to soy proteins has become relevant in a restricted proportion of milk allergic pediatric patients treated with soy formulae as a dairy substitute, because of the cross-allergenicity described between soy and milk proteins. We have previously identified several cross-reactive allergens between milk and soy that may explain this intolerance. The purpose of the present work was to identify epitopes in the purified αS1-casein and the recombinant soy allergen Gly m 5.0101 (Gly m 5) using an α-casein-specific monoclonal antibody (1D5 mAb) through two different approaches for epitope mapping, to understand cross-reactivity between milk and soy. The 1D5 mAb was immobilized onto magnetic beads, incubated with the peptide mixture previously obtained by enzymatic digestion of the allergens, and the captured peptides were identified by MALDI-TOF MS analysis. On a second approach, the peptide mixture was resolved by RP-HPLC and immunodominant peptides were identified by dot blot with the mAb. Finally, recognized peptides were sequenced by MALDI-TOF MS. This novel MS based approach led us to identify and characterize four peptides on α-casein and three peptides on Gly m 5 with a common core motif. Information obtained from these cross-reactive epitopes allows us to gain valuable insight into the molecular mechanisms of cross-reactivity, to further develop new and more effective vaccines for food allergy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Visualization and Classification of Deeply Seated Collateral Networks in Moyamoya Angiopathy with 7T MRI.

PubMed

Matsushige, T; Kraemer, M; Sato, T; Berlit, P; Forsting, M; Ladd, M E; Jabbarli, R; Sure, U; Khan, N; Schlamann, M; Wrede, K H

2018-06-07

Collateral networks in Moyamoya angiopathy have a complex angioarchitecture difficult to comprehend on conventional examinations. This study aimed to evaluate morphologic patterns and the delineation of deeply seated collateral networks using ultra-high-field MRA in comparison with conventional DSA. Fifteen white patients with Moyamoya angiopathy were investigated in this prospective trial. Sequences acquired at 7T were TOF-MRA with 0.22 × 0.22 × 0.41 mm 3 resolution and MPRAGE with 0.7 × 0.7 × 0.7 mm 3 resolution. Four raters evaluated the presence of deeply seated collateral networks and image quality in a consensus reading of DSA, TOF-MRA, and MPRAGE using a 5-point scale in axial source images and maximum intensity projections. Delineation of deeply seated collateral networks by different imaging modalities was compared by means of the McNemar test, whereas image quality was compared using the Wilcoxon signed-rank test. The relevant deeply seated collateral networks were classified into 2 categories and 6 pathways. A total of 100 collateral networks were detected on DSA; 106, on TOF-MRA; and 73, on MPRAGE. Delineation of deeply seated collateral networks was comparable between TOF-MRA and DSA ( P = .25); however, both were better than MPRAGE ( P < .001). This study demonstrates excellent delineation of 6 distinct deeply seated collateral network pathways in Moyamoya angiopathy in white adults using 7T TOF-MRA, comparable to DSA. © 2018 by American Journal of Neuroradiology.

Identification and susceptibility testing of microorganism by direct inoculation from positive blood culture bottles by combining MALDI-TOF and Vitek-2 Compact is rapid and effective.

PubMed

Romero-Gómez, María-Pilar; Gómez-Gil, Rosa; Paño-Pardo, Jose Ramón; Mingorance, Jesús

2012-12-01

The objective of this study was to evaluate the reliability and accuracy of the combined use of MALDI-TOF MS bacterial identification and the Vitek-2 Compact antimicrobial susceptibility testing (AST) directly from positive blood cultures. Direct identification by MALDI-TOF MS and AST were performed in parallel to the standard methods in all positively flagged blood cultures bottles during the study period. Three hundred and twenty four monomicrobial positive blood cultures were included in the present study, with 257 Gram-negative and 67 Gram-positive isolates. MALDI-TOF MS identification directly from blood bottles reported the correct identification for Enterobacteriaceae in 97.7%, non-fermentative Gram-negative bacilli 75.0%, Staphylococcus aureus 75.8%, coagulase negative staphylococci 63.3% and enterococci 63.3%. A total 6156 isolate/antimicrobial agent combinations were tested. Enterobacteriaceae group and non-fermentative Gram-negative Bacilli showed an agreement of 96.67% and 92.30%, respectively, for the Gram-positive cocci the overall agreement found was 97.84%. We conclude that direct identification by MALDI-TOF and inoculation of Vitek-2 Compact AST with positive blood culture bottles yielded very good results and decreased time between initial inoculation of blood culture media and determination of the antibiotic susceptibility for Gram-negative rods and Gram-positive cocci causing bacteremia. Copyright © 2012 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Assessment of acquisition protocols for routine imaging of Y-90 using PET/CT

PubMed Central

2013-01-01

Background Despite the early theoretical prediction of the 0+-0+ transition of 90Zr, 90Y-PET underwent only recently a growing interest for the development of imaging radioembolization of liver tumors. The aim of this work was to determine the minimum detectable activity (MDA) of 90Y by PET imaging and the impact of time-of-flight (TOF) reconstruction on detectability and quantitative accuracy according to the lesion size. Methods The study was conducted using a Siemens Biograph® mCT with a 22 cm large axial field of view. An IEC torso-shaped phantom containing five coplanar spheres was uniformly filled to achieve sphere-to-background ratios of 40:1. The phantom was imaged nine times in 14 days over 30 min. Sinograms were reconstructed with and without TOF information. A contrast-to-noise ratio (CNR) index was calculated using the Rose criterion, taking partial volume effects into account. The impact of reconstruction parameters on quantification accuracy, detectability, and spatial localization of the signal was investigated. Finally, six patients with hepatocellular carcinoma and four patients included in different 90Y-based radioimmunotherapy protocols were enrolled for the evaluation of the imaging parameters in a clinical situation. Results The highest CNR was achieved with one iteration for both TOF and non-TOF reconstructions. The MDA, however, was found to be lower with TOF than with non-TOF reconstruction. There was no gain by adding TOF information in terms of CNR for concentrations higher than 2 to 3 MBq mL−1, except for infra-centimetric lesions. Recovered activity was highly underestimated when a single iteration or non-TOF reconstruction was used (10% to 150% less depending on the lesion size). The MDA was estimated at 1 MBq mL−1 for a TOF reconstruction and infra-centimetric lesions. Images from patients treated with microspheres were clinically relevant, unlike those of patients who received systemic injections of 90Y. Conclusions Only one iteration and TOF were necessary to achieve an MDA around 1 MBq mL−1 and the most accurate localization of lesions. For precise quantification, at least three iterations gave the best performance, using TOF reconstruction and keeping an MDA of roughly 1 MBq mL−1. One and three iterations were mandatory to prevent false positive results for quantitative analysis of clinical data. Trial registration http://IDRCB 2011-A00043-38 P101103 PMID:23414629

Chromatogram-Bioactivity Correlation-Based Discovery and Identification of Three Bioactive Compounds Affecting Endothelial Function in Ginkgo Biloba Extract.

PubMed

Liu, Hong; Tan, Li-Ping; Huang, Xin; Liao, Yi-Qiu; Zhang, Wei-Jian; Li, Pei-Bo; Wang, Yong-Gang; Peng, Wei; Wu, Zhong; Su, Wei-Wei; Yao, Hong-Liang

2018-05-03

Discovery and identification of three bioactive compounds affecting endothelial function in Ginkgo biloba Extract (GBE) based on chromatogram-bioactivity correlation analysis. Three portions were separated from GBE via D101 macroporous resin and then re-combined to prepare nine GBE samples. 21 compounds in GBE samples were identified through UFLC-DAD-Q-TOF-MS/MS. Correlation analysis between compounds differences and endothelin-1 (ET-1) in vivo in nine GBE samples was conducted. The analysis results indicated that three bioactive compounds had close relevance to ET-1: Kaempferol-3- O -α-l-glucoside, 3- O -{2- O -{6- O -[P-OH-trans-cinnamoyl]-β-d-glucosyl}-α-rhamnosyl} Quercetin isomers, and 3- O -{2- O -{6- O -[P-OH-trans-cinnamoyl]-β-d-glucosyl}-α-rhamnosyl} Kaempferide. The discovery of bioactive compounds could provide references for the quality control and novel pharmaceuticals development of GRE. The present work proposes a feasible chromatogram-bioactivity correlation based approach to discover the compounds and define their bioactivities for the complex multi-component systems.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0043: Deformation and Texture Development During Hot Working of Titanium

DTIC Science & Technology

2008-04-01

Hot Working of Titanium 5a. CONTRACT NUMBER F33615-03-D-5801-0043 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61202F 6 . AUTHOR(S) A.A...micrographs and thus to correlate microstructural features and texture data [3- 6 ]. For instance, Germain, et al. [3, 4 ] linked local orientations...microstructures can be developed in alpha/beta titanium alloys by TMP [2- 4 ], namely, fully lamellar, fully equiaxed, and duplex (bi-modal). A mixture

Sodium accumulation at potential-induced degradation shunted areas in polycrystalline silicon modules

DOE PAGES

Harvey, Steven P.; Aguiar, Jeffery A.; Hacke, Peter; ...

2016-09-19

Here, we investigated potential-induced degradation (PID) in silicon mini-modules that were subjected to accelerated stressing to induce PID conditions. Shunted areas on the cells were identified with photoluminescence and dark lock-in thermography (DLIT) imaging. The identical shunted areas were then analyzed via time-of-flight secondary-ion mass spectrometry (TOFSIMS) imaging, 3-D tomography, and high-resolution transmission electron microscopy. The TOF-SIMS imaging indicates a high concentration of sodium in the shunted areas, and 3-D tomography reveals that the sodium extends more than 2 um from the surface below shunted regions. Transmission electron microscopy investigation reveals that a stacking fault is present at an areamore » identified as shunted by DLIT imaging. After the removal of surface sodium, tomography reveals persistent sodium present around the junction depth of 300 nm and a drastic difference in sodium content at the junction when comparing shunted and nonshunted regions.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Steven P.; Aguiar, Jeffery A.; Hacke, Peter

Here, we investigated potential-induced degradation (PID) in silicon mini-modules that were subjected to accelerated stressing to induce PID conditions. Shunted areas on the cells were identified with photoluminescence and dark lock-in thermography (DLIT) imaging. The identical shunted areas were then analyzed via time-of-flight secondary-ion mass spectrometry (TOFSIMS) imaging, 3-D tomography, and high-resolution transmission electron microscopy. The TOF-SIMS imaging indicates a high concentration of sodium in the shunted areas, and 3-D tomography reveals that the sodium extends more than 2 um from the surface below shunted regions. Transmission electron microscopy investigation reveals that a stacking fault is present at an areamore » identified as shunted by DLIT imaging. After the removal of surface sodium, tomography reveals persistent sodium present around the junction depth of 300 nm and a drastic difference in sodium content at the junction when comparing shunted and nonshunted regions.« less

Analysis of extracellular proteins of Aspergillus oryzae grown on soy sauce koji.

PubMed

Liang, Yanchang; Pan, Li; Lin, Ying

2009-01-01

Aspergillus oryzae AS 3.951 is widely used in Chinese soy sauce manufacture, but little is known about the profiles of the extracellular proteins from the culture of soybean koji. In this study, we carried out MALDI-TOF/TOF MS analysis of extracellular proteins during koji culture. Besides well-known proteins (TAA and Oryzin), a variety of aminopeptidase and proteases were identical at the proteome level. This suggests that A. oryzae AS 3.951 has a powerful capacity to digest soybean protein.

Registration of partially overlapping surfaces for range image based augmented reality on mobile devices

NASA Astrophysics Data System (ADS)

Kilgus, T.; Franz, A. M.; Seitel, A.; Marz, K.; Bartha, L.; Fangerau, M.; Mersmann, S.; Groch, A.; Meinzer, H.-P.; Maier-Hein, L.

2012-02-01

Visualization of anatomical data for disease diagnosis, surgical planning, or orientation during interventional therapy is an integral part of modern health care. However, as anatomical information is typically shown on monitors provided by a radiological work station, the physician has to mentally transfer internal structures shown on the screen to the patient. To address this issue, we recently presented a new approach to on-patient visualization of 3D medical images, which combines the concept of augmented reality (AR) with an intuitive interaction scheme. Our method requires mounting a range imaging device, such as a Time-of-Flight (ToF) camera, to a portable display (e.g. a tablet PC). During the visualization process, the pose of the camera and thus the viewing direction of the user is continuously determined with a surface matching algorithm. By moving the device along the body of the patient, the physician is given the impression of looking directly into the human body. In this paper, we present and evaluate a new method for camera pose estimation based on an anisotropic trimmed variant of the well-known iterative closest point (ICP) algorithm. According to in-silico and in-vivo experiments performed with computed tomography (CT) and ToF data of human faces, knees and abdomens, our new method is better suited for surface registration with ToF data than the established trimmed variant of the ICP, reducing the target registration error (TRE) by more than 60%. The TRE obtained (approx. 4-5 mm) is promising for AR visualization, but clinical applications require maximization of robustness and run-time.

Time-of-flight magnetic resonance angiography imaging of a residual arteriovenous malformation nidus after Onyx embolization for stereotactic radiosurgery planning. Technical note.

PubMed

Loy, David N; Rich, Keith M; Simpson, Joseph; Dorward, Ian; Santanam, Lakshmi; Derdeyn, Colin P

2009-05-01

This report demonstrates that time-of-flight (TOF) MR angiography is a useful adjunct for planning stereotactic radiosurgery (SRS) of large arteriovenous malformations (AVMs) after staged embolization with Onyx. Onyx (ethylene vinyl copolymer), a recently approved liquid embolic agent, has been increasingly used to exclude portions of large AVMs from the parent circulation prior to SRS. Limiting SRS to regions of persistent arteriovenous shunting and excluding regions eliminated by embolization may reduce unnecessary radiation doses to eloquent brain structures. However, SRS dosimetry planning presents unique challenges after Onyx embolization because it creates extensive artifacts on CT scans, and it cannot be delineated from untreated nidus on standard MR sequences. During the radiosurgery procedure, MR images were obtained using a GE Signa 1.5-T unit. Standard axial T2 fast spin echo high-resolution images (TR 3000 msec, TE 108 msec, slice thickness 2.5 mm) were generated for optimal visualization of brain tissue and AVM flow voids. The 3D TOF MR angiography images of the circle of Willis and vertebral arteries were subsequently obtained to visualize AVM regions embolized with Onyx (TR 37 msec, TE 6.9 msec, flip angle 20 degrees). Adjunct TOF MR angiography images demonstrated excellent contrast between nidus embolized with Onyx and regions of persistent arteriovenous shunting within a large AVM prior to SRS. Additional information derived from these sequences resulted in substantial adjustments to the treatment plan and an overall reduction in the treated tissue volume.

MALDI-TOF MS identification of anaerobic bacteria: assessment of pre-analytical variables and specimen preparation techniques.

PubMed

Hsu, Yen-Michael S; Burnham, Carey-Ann D

2014-06-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a tool for identifying clinically relevant anaerobes. We evaluated the analytical performance characteristics of the Bruker Microflex with Biotyper 3.0 software system for identification of anaerobes and examined the impact of direct formic acid (FA) treatment and other pre-analytical factors on MALDI-TOF MS performance. A collection of 101 anaerobic bacteria were evaluated, including Clostridium spp., Propionibacterium spp., Fusobacterium spp., Bacteroides spp., and other anaerobic bacterial of clinical relevance. The results of our study indicate that an on-target extraction with 100% FA improves the rate of accurate identification without introducing misidentification (P<0.05). In addition, we modify the reporting cutoffs for the Biotyper "score" yielding acceptable identification. We found that a score of ≥1.700 can maximize the rate of identification. Of interest, MALDI-TOF MS can correctly identify anaerobes grown in suboptimal conditions, such as on selective culture media and following oxygen exposure. In conclusion, we report on a number of simple and cost-effective pre- and post-analytical modifications could enhance MALDI-TOF MS identification for anaerobic bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Towards dense volumetric pancreas segmentation in CT using 3D fully convolutional networks

NASA Astrophysics Data System (ADS)

Roth, Holger; Oda, Masahiro; Shimizu, Natsuki; Oda, Hirohisa; Hayashi, Yuichiro; Kitasaka, Takayuki; Fujiwara, Michitaka; Misawa, Kazunari; Mori, Kensaku

2018-03-01

Pancreas segmentation in computed tomography imaging has been historically difficult for automated methods because of the large shape and size variations between patients. In this work, we describe a custom-build 3D fully convolutional network (FCN) that can process a 3D image including the whole pancreas and produce an automatic segmentation. We investigate two variations of the 3D FCN architecture; one with concatenation and one with summation skip connections to the decoder part of the network. We evaluate our methods on a dataset from a clinical trial with gastric cancer patients, including 147 contrast enhanced abdominal CT scans acquired in the portal venous phase. Using the summation architecture, we achieve an average Dice score of 89.7 +/- 3.8 (range [79.8, 94.8])% in testing, achieving the new state-of-the-art performance in pancreas segmentation on this dataset.

MALDI-TOF Mass Spectrometry for the Detection and Differentiation of Entamoeba histolytica and Entamoeba dispar

PubMed Central

Calderaro, Adriana; Piergianni, Maddalena; Buttrini, Mirko; Montecchini, Sara; Piccolo, Giovanna; Gorrini, Chiara; Rossi, Sabina; Chezzi, Carlo; Arcangeletti, Maria Cristina; Medici, Maria Cristina; De Conto, Flora

2015-01-01

Detection of Entamoeba histolytica and its differentiation from Entamoeba dispar is an important goal of the clinical parasitology laboratory. The aim of this study was the identification and differentiation of E. histolytica and E. dispar by MALDI-TOF MS, in order to evaluate the application of this technique in routine diagnostic practice. MALDI-TOF MS was applied to 3 amebic reference strains and to 14 strains isolated from feces that had been differentiated by molecular methods in our laboratory. Protein extracts from cultures of these strains (axenic cultures for the 3 reference strains and monoxenic cultures for the 14 field isolates) were analyzed by MALDI-TOF MS and the spectra obtained were analyzed by statistical software. Five peaks discriminating between E. histolytica and E. dispar reference strains were found by protein profile analysis: 2 peaks (8,246 and 8,303 Da) specific for E. histolytica and 3 (4,714; 5,541; 8,207 Da) for E. dispar. All clinical isolates except one showed the discriminating peaks expected for the appropriate species. For 2 fecal samples from which 2 strains (1 E. histolytica and 1 E. dispar) out of the 14 included in this study were isolated, the same discriminating peaks found in the corresponding isolated amebic strains were detected after only 12h (E. histolytica) and 24h (E. dispar) of incubation of the fecal samples in Robinson’s medium without serum. Our study shows that MALDI-TOF MS can be used to discriminate between E. histolytica and E. dispar using in vitro xenic cultures and it also could have potential for the detection of these species in clinical samples. PMID:25874612

Characterization of the upper pouch tracheo-oesophageal fistula in oesophageal atresia.

PubMed

Summerour, Virginia; Stevens, Paul S; Lander, Anthony D; Singh, Michael; Soccorso, Giampiero; Arul, G Suren

2017-02-01

A small proportion of infants with oesophageal atresia (OA) are thought to have a proximal tracheoesophageal fistula (TOF). Failure to recognize these can hamper mobilization of the upper pouch and lead to life-threatening episodes of aspiration once oral feeding starts. We reviewed our experience of upper pouch fistulae to identify characteristic features of proximal TOF. A retrospective review of TOF/OA patient notes and bronchoscopy photographs and videos, identified from our database from 01/01/2006 to 12/31/2015, was performed. Eight (6.1%) infants were identified (M:F 5:3) from a total population of 131 newly diagnosed TOF/OA infants during the period. Their median gestational age was 33 (range 28-39) weeks, and median birth weight was 1647g (range 1100-3400g). Five were initially diagnosed with pure OA and 3 with a distal TOF. All patients underwent rigid bronchoscopy at the initial surgery but only one proximal fistula was identified. The 7 missed proximal fistulae were subsequently found either during on-table oesophagograms for gap assessment (n=2), at the time of thoracotomy when mobilizing the upper pouch (n=3), or during subsequent bronchoscopy for symptoms post OA repair (n=2). Two patients needed a further operation to divide the fistula. Review of the bronchoscopy videos identified four characteristic differences between upper and lower pouch fistulae. Proximal fistulae are found just distal to the vocal cords, are very small, often no more than a pit, do not open and close with ventilation, and are best identified by insufflation of the esophagus. Upper pouch fistulae are relatively easy to miss because of different characteristics compared with H-type or distal fistulae that have not previously been mentioned in the literature. level IV. Copyright © 2016. Published by Elsevier Inc.

3D model assisted fully automated scanning laser Doppler vibrometer measurements

NASA Astrophysics Data System (ADS)

Sels, Seppe; Ribbens, Bart; Bogaerts, Boris; Peeters, Jeroen; Vanlanduit, Steve

2017-12-01

In this paper, a new fully automated scanning laser Doppler vibrometer (LDV) measurement technique is presented. In contrast to existing scanning LDV techniques which use a 2D camera for the manual selection of sample points, we use a 3D Time-of-Flight camera in combination with a CAD file of the test object to automatically obtain measurements at pre-defined locations. The proposed procedure allows users to test prototypes in a shorter time because physical measurement locations are determined without user interaction. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. The proposed method is illustrated with vibration measurements of an unmanned aerial vehicle

Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis).

PubMed

Han, Hua; Sun, Xiaomei; Xie, Yunhui; Feng, Jian; Zhang, Shougong

2014-11-26

Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is known about the regulation of adventitious root development in larch hybrids. 454 GS FLX Titanium technology represents a new method for characterizing the transcriptomes of non-model species. This method can be used to identify differentially expressed genes, and then two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analyses can be used to analyze their corresponding proteins. In this study, we analyzed semi-lignified cuttings of two clones of L. kaempferi × L. olgensis with different rooting capacities to study the molecular basis of adventitious root development. We analyzed two clones; clone 25-5, with strong rooting capacity, and clone 23-12, with weak rooting capacity. We constructed four cDNA libraries from 25-5 and 23-12 at two development stages. Sequencing was conducted using the 454 pyrosequencing platform. A total of 957832 raw reads was produced; 95.07% were high-quality reads, and were assembled into 45137 contigs and 61647 singletons. The functions of the unigenes, as indicated by their Gene Ontology annotation, included diverse roles in the molecular functions, biological processes, and cellular component categories. We analyzed 75 protein spots (-fold change ≥ 2, P ≤ 0.05) by 2D-DIGE, and identified the differentially expressed proteins using MALDI-TOF/TOF MS. A joint analysis of transcriptome and proteome showed genes related to two pathways, polyamine synthesis and stress response, might play an important role on adventitious root development. These results provide fundamental and important information for research on the molecular mechanism of adventitious root development. We also demonstrated for the first time the combined use of two important technologies as a powerful approach to advance research on non-model, but otherwise important, larch species.

Structural and functional characterization of proteinase inhibitors from seeds of Cajanus cajan (cv. ICP 7118).

PubMed

Swathi, Marri; Lokya, Vadthya; Swaroop, Vanka; Mallikarjuna, Nalini; Kannan, Monica; Dutta-Gupta, Aparna; Padmasree, Kollipara

2014-10-01

Proteinase inhibitors (C11PI) from mature dry seeds of Cajanus cajan (cv. ICP 7118) were purified by chromatography which resulted in 87-fold purification and 7.9% yield. SDS-PAGE, matrix assisted laser desorption ionization time-of-flight (MALDI-TOF/TOF) mass spectrum and two-dimensional (2-D) gel electrophoresis together resolved that C11PI possessed molecular mass of 8385.682 Da and existed as isoinhibitors. However, several of these isoinhibitors exhibited self association tendency to form small oligomers. All the isoinhibitors resolved in Native-PAGE and 2-D gel electrophoresis showed inhibitory activity against bovine pancreatic trypsin and chymotrypsin as well as Achaea janata midgut trypsin-like proteases (AjPs), a devastating pest of castor plant. Partial sequences of isoinhibitor (pI 6.0) obtained from MALDI-TOF/TOF analysis and N-terminal sequencing showed 100% homology to Bowman-Birk Inhibitors (BBIs) of leguminous plants. C11PI showed non-competitive inhibition against trypsin and chymotrypsin. A marginal loss (<15%) in C11PI activity against trypsin at 80 (°)C and basic pH (12.0) was associated with concurrent changes in its far-UV CD spectra. Further, in vitro assays demonstrated that C11PI possessed significant inhibitory potential (IC50 of 78 ng) against AjPs. On the other hand, in vivo leaf coating assays demonstrated that C11PI caused significant mortality rate with concomitant reduction in body weight of both larvae and pupae, prolonged the duration of transition from larva to pupa along with formation of abnormal larval-pupal and pupal-adult intermediates. Being smaller peptides, it is possible to express C11PI in castor to protect them against its devastating pest A. janata. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

The Dermatophagoides farinae group 22 allergen: cloning and expression in Escherichia coli.

PubMed

Cui, Yu-bao; Cai, Hong-xing; Zhou, Ying; Wang, Nan; Yu, Li-li; Yang, Li; Zhang, Cheng-bo

2015-09-01

Dermatophagoides farinae (Hughes) (Acari: Pyroglyphidae) and other domestic mites produce allergens that affect people worldwide. Here, the complementary DNA (cDNA) coding for group 22 allergen of D. farinae (Der f 22) from China was cloned, sequenced, and expressed successfully. The cDNA encoding Der f 22 was synthesized by reverse transcription polymerase chain reaction (RT-PCR), then ligated to the pCold-TF for expression in Escherichia coli BL21 cells. The purified recombinant fusion protein was identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Western-blotting, and tandem matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF/TOF). The full-length cDNA comprised 468 nucleotides and was 99.57% (466/468) identical with the reference sequence (GenBank: DQ643992). After the plasmid pCold-TF-Der f 22 was transformed into E. coli BL21 and expressed with the induction of IPTG, SDS-PAGE showed a specific band for the recombinant fusion protein. The recombinant fusion protein, which was purified by chromatography, bound with a His-tagged antibody by Western blotting. MALDI-TOF/TOF mass spectrometry revealed that the structure of the recombinant protein was identical to the predicted Der f 22 structure. The hydrophilic protein contains a signal peptide of 20 amino acids, and the mature Der f 22 consists of 135 amino acid residues with a molecular weight of 14.7 kDa and theoretical isoelectric points (pI) of 6.38. Its secondary structure comprises an alpha helix (38.5%), beta-sheet (45.9%), random coils (11.85%), and beta-turns (11.1%). This work represents the first reported full-length sequence and successful cloning of Der f 22 from D. farinae in China; bioinformatics analysis can be used to further study the allergenicity and clinical utility of the recombinant Der f 22. © 2015 ARS-AAOA, LLC.

Wavelength-independent constant period spin-echo modulated small angle neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sales, Morten, E-mail: lsp260@alumni.ku.dk; Plomp, Jeroen; Bouwman, Wim

2016-06-15

Spin-Echo Modulated Small Angle Neutron Scattering (SEMSANS) in Time-of-Flight (ToF) mode has been shown to be a promising technique for measuring (very) small angle neutron scattering (SANS) signals and performing quantitative Dark-Field Imaging (DFI), i.e., SANS with 2D spatial resolution. However, the wavelength dependence of the modulation period in the ToF spin-echo mode has so far limited the useful modulation periods to those resolvable with the limited spatial resolution of the detectors available. Here we present our results of an approach to keep the period of the induced modulation constant for the wavelengths utilised in ToF. This is achieved bymore » ramping the magnetic fields in the coils responsible for creating the spatially modulated beam in synchronisation with the neutron pulse, thus keeping the modulation period constant for all wavelengths. Such a setup enables the decoupling of the spatial detector resolution from the resolution of the modulation period by the use of slits or gratings in analogy to the approach in grating-based neutron DFI.« less

Seven-tesla time-of-flight angiography using a 16-channel parallel transmit system with power-constrained 3-dimensional spoke radiofrequency pulse design

PubMed Central

Schmitter, Sebastian; Wu, Xiaoping; Auerbach, Edward J.; Adriany, Gregor; Pfeuffer, Josef; Hamm, Michael; Ugurbil, Kamil; Van de Moortele, Pierre-Francois

2015-01-01

Objectives Ultra high magnetic fields of ≥7 Tesla have proven to significantly enhance the contrast in time-of-flight (TOF) imaging, one of the most commonly used non-contrast enhanced MR angiography techniques. Compared to lower field strength, however, the required RF power is increased at 7 Tesla and the contrast obtained with a conventional head transmit RF coil is typically spatially heterogeneous. In this work we address the contrast heterogeneity in multi-slab TOF acquisitions by optimizing the excitation flip angle homogeneity while constraining the RF power using 3D tailored RF pulses (“spokes”) with a 16 channel parallel transmission system and a 16 channel transceiver head coil. Material and Methods We investigate in simulations and in-vivo experiments flip angle homogeneity and angiogram quality with a same 3-slab TOF protocol for different excitations including 1-, 2- and 3-spoke parallel transmit RF pulses and compare the results with a circularly polarized (CP) phase setting similar to a birdcage excitation. B1 and B0 calibration maps were obtained in multiple slices and the RF pulse for each slab was designed based on 3 calibration slices located at the bottom/middle/top of each slab respectively. By design, all excitations were computed to generate the same total RF power for the same flip angle. In 8 subjects we quantify the excitation homogeneity and the distribution of the RF power to individual channels. In addition, we investigate the consequences of local flip angle variations at the junction between adjacent slabs as well as the impact of ΔB0 on image quality. Results The flip angle heterogeneity, expressed as the coefficient of variation, averaged over all volunteers and all slabs could be reduced from 29.4% for CP mode excitation to 14.1% for a 1-spoke excitation and to 7.3% for a 2-spoke excitations. A separate detailed analysis shows only a marginal improvement for 3-spoke compared to the 2-spoke excitation. The strong improvement in flip angle homogeneity particularly impacted the junction between adjacent TOF slabs, where significant residual artifacts observed with 1-spoke excitation could be efficiently mitigated using a 2-spoke excitation with same RF power and same average flip angle. Even though the total RF power is maintained at the same level than in CP mode excitation, the energy distribution is fairly heterogeneous through the 16 transmit channels for 1- and 2-spoke excitation, with the highest energy for one channel being a factor of 2.4 (1-spoke) and 2.2 (2-spoke) higher than in CP mode. In vivo experiments demonstrate the necessity of including ΔB0 spatial variations during 2-spoke RF pulse design, in particular in areas with strong local susceptibility variations such as the lower frontal lobe. Conclusion Significant improvement in excitation fidelity leading to improved TOF contrast, particularly in the brain periphery, as well as smooth slab transitions can be achieved with 2-spoke excitation while maintaining the same excitation energy as in CP mode. These results suggest that expanding parallel transmit methods, including the use of multi-dimensional spatially selective excitation, will also be very beneficial for other techniques, such as perfusion imaging. PMID:24598439

Composition and structure of surfaces by time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Ahn, Jeongheon

1997-10-01

Time-of-flight scattering and recoiling spectrometry (TOF-SARS) was applied to characterize surface structures in order to understand the chemical and physical phenomena on various surfaces. The combination of TOF-SARS, LEED, and classical ion trajectory simulations has allowed characterization of the elemental composition in the outermost atomic layers, surface symmetry, and possible reconstruction or relaxation. The composition and structure of the CdS\\{0001\\}-(1 x 1) and CdS\\{000bar1\\}-(1 x 1) surfaces were investigated. The termination layer of each surface was determined by grazing incidence TOF-SARS. Both (1 x 1) surfaces are bulk-terminated without any reconstruction or relaxation detected by TOF-SARS. Each surface has two domains which are rotated by 60sp° from each other and there exist steps on both surfaces. The CdS\\{0001\\}-(1 x 1) surface is stabilized by O and H covering half a monolayer which are structurally ordered on the surface, while the O and H on the CdS\\{000bar1\\}-(1 x 1) stabilize the surface without ordering. The study of GaN\\{000bar1\\}-(1 x 1) shows the bulk-termination of the surface with no detectable reconstruction or relaxation. The surface is terminated in a N layer with Ga in the 2sp{nd}-layer. H atoms are bound to the outermost N atoms with a coverage of ˜3/4 monolayer and protrude outward from the surface. The surface termination, composition and structure of the Alsb2Osb3 (sapphire) were examined. The surface relaxation was studied quantitatively using classical ion trajectory simulations along with TOF-SARS. The surface undergoes 1sp{st}{-}2sp{nd}-layer relaxation as large as 0.5 A from the bulk value resulting in near coplanarity of Al and O atoms. The reconstruction of the Ni\\{100\\}-(2 x 2)-C surface was studied by TOF-SARS. The surface contained 80% of the (2 x 2)p4g phase and 20% of the unreconstructed (2 x 2) phase. The displacement of Ni atoms was determined by comparing the experimental and simulated results.

Potato wound-healing tissues: A rich source of natural antioxidant molecules with potential for food preservation.

PubMed

Dastmalchi, Keyvan; Wang, Isabel; Stark, Ruth E

2016-11-01

The need for safe, effective preservatives is a prominent issue in the food and drug industries, reflecting demand for natural alternatives to synthetic chemicals viewed as harmful to consumers and the environment. Thus, this study determined the identities and scavenging capacities of antioxidant metabolites produced as a response to potato tuber wounding, using activity-guided fractionation of polar extracts from a Yukon Gold cultivar that had previously exhibited exceptionally high radical-scavenging activity. Activity-guided fractionation using the ABTS(+) radical scavenging assay and LC-MS with TOF-MS for compositional analysis of the most potent antioxidant fractions yielded identification of nine constituents: coumaroylputrescine; feruloylquinic acid; isoferuloylputrescine; ferulic acid; 22,25-dimethoxy-3-[[2,3,4-tri-O-methyl-6-O-(2,3,4,6-tetra-O-methyl-β-d-glucopyranosyl)-β-d-glucopyranosyl]oxy]-(3β)-lanost-9(11)-en-24-one; 4-(2Z)-2-decen-1-yl-5-[1-(4-hydroxyphenyl)decyl]-1,2-benzenediol; 8-[(2E)-3,7-dimethyl-2,6-octadien-1-yl]-5-hydroxy-2,8-dimethyl-6-(3-methyl-2-buten-1-yl)-2H-1-benzopyran-4,7(3H,8H)-dione; 3-[(2-O-β-d-glucopyranosyl-β-d-glucopyranosyl)oxy]-20-[(6-O-β-d-xylopyranosyl-β-d-glucopyranosyl)oxy]-dammar-24-en-19-al; (3β)-28-oxo-28-(phenylmethoxy)oleanan-3-yl 2-O-β-d-galactopyranosyl-3-O-(phenylmethyl)-, butyl ester β-d-glucopyranosiduronic acid. A positive correlation was observed between the scavenging activities and the polarities of the active fractions. The antioxidant capacities of the fractions were also characterised by monitoring the activity throughout a 45-minute assay period. Copyright © 2016 Elsevier Ltd. All rights reserved.

Potato Wound-Healing Tissues: A Rich Source of Natural Antioxidant Molecules with Potential for Food Preservation

PubMed Central

Dastmalchi, Keyvan; Wang, Isabel; Stark, Ruth E.

2016-01-01

The need for safe, effective preservatives is a prominent issue in the food and drug industries, reflecting demand for natural alternatives to synthetic chemicals viewed as harmful to consumers and the environment. Thus, this study determined the identities and scavenging capacities of antioxidant metabolites produced as a response to potato tuber wounding, using activity-guided fractionation of polar extracts from a Yukon Gold cultivar that had previously exhibited exceptionally high radical-scavenging activity. Activity-guided fractionation using the ABTS•+ radical scavenging assay and LC-MS with TOF-MS for compositional analysis of the most potent antioxidant fractions yielded identification of nine constituents: coumaroylputrescine; feruloylquinic acid; isoferuloylputrescine; ferulic acid; 22,25-dimethoxy-3-[[2,3,4-tri-O-methyl-6-O-(2,3,4,6-tetra-O-methyl-β-D-glucopyranosyl)-β-D-glucopyranosyl]oxy]-(3β)-lanost-9(11)-en-24-one; 4-(2Z)-2-decen-1-yl-5-[1-(4-hydroxyphenyl)decyl]-1,2-benzenediol; 8-[(2E)-3,7-dimethyl-2,6-octadien-1-yl]-5-hydroxy-2,8-dimethyl-6-(3-methyl-2-buten-1-yl)-2H-1-benzopyran-4,7(3H,8H)-dione; 3-[(2-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy]-20-[(6-O-β-D-xylopyranosyl-β-D-glucopyranosyl)oxy]-dammar-24-en-19-al; (3β)-28-oxo-28-(phenylmethoxy)oleanan-3-yl 2-O-β-D-galactopyranosyl-3-O-(phenylmethyl)-, butyl ester β-D-glucopyranosiduronic acid. A positive correlation was observed between the scavenging activities and the polarities of the active fractions. The antioxidant capacities of the fractions were also characterised by monitoring the activity throughout a 45-minute assay period. PMID:27211673

Detection of choline and phosphatidic acid (PA) catalyzed by phospholipase D (PLD) using MALDI-QIT-TOF/MS with 9-aminoacridine matrix.

PubMed

Park, Kyung-Eui; Kim, Jun-Dal; Nagashima, Yusuke; Kako, Koichiro; Daitoku, Hiroaki; Matsui, Motoki; Park, Gwi Gun; Fukamizu, Akiyoshi

2014-01-01

Phospholipase D (PLD) catalyzes the hydrolysis of phosphatidylcholine (PC), the most abundant phospholipids of plasma membrane, resulting in the production of choline and phosphatidic acid (PA). Choline is a precursor of the neurotransmitter acetylcholine, whereas PA functions as an intracellular lipid mediator of diverse biological functions. For assessing PLD activity in vitro, PLD-derived choline has been often analyzed with radioactive or non-radioactive methods. In this study, we have developed a new method for detecting choline and PA with MALDI-QIT-TOF/MS by using 9-aminoacridine as a matrix. The standard calibration curves showed that choline and PA could be detected with linearity over the range from 0.05 and 1 pmol, respectively. Importantly, this method enables the concomitant detection of choline and PA as a reaction product of PC hydrolysis by PLD2 proteins. Thus, our simple and direct method would be useful to characterize the enzymatic properties of PLD, thereby providing insight into mechanisms of PLD activation.

Recombinant overexpression of camel hepcidin cDNA in Pichia pastoris: purification and characterization of the polyHis-tagged peptide HepcD-His.

PubMed

Boumaiza, Mohamed; Chahed, Haifa; Ezzine, Aymen; Jaouan, Maryse; Gianoncelli, Alessandra; Longhi, Giovanna; Carmona, Fernando; Arosio, Paolo; Sari, Marie-Agnès; Marzouki, Mohamed Nejib

2017-01-01

Hepcidin, a liver-expressed antimicrobial peptide, has been demonstrated to act as an iron regulatory hormone as well as to exert a wide spectrum of antimicrobial activity. The aim of this work was the expression, as secreted peptide, purification, and characterization of a new recombinant polyHis-tagged camel hepcidin (HepcD-His) in yeast Pichia pastoris. The use of this eukaryotic expression system, for the production of HepcD-His, having 6 histidine residues at its C terminus, was simpler and more efficient compared with the use of the prokaryotic system Escherichia coli. Indeed, a single purification step was required to isolate the soluble hepcidin with purity estimated more that 94% and a yield of 2.8 against 0.2 mg/L for the E coli system. Matrix-assisted laser desorption/ionization time-of-flight (TOF)/TOF mass spectrometry of the purified HepcD-His showed 2 major peaks at m/z 4524.64 and 4634.56 corresponding to camel hepcidin with 39 and 40 amino acids. Evaluation of disulfide bond connectivity with the Ellman method showed an absence of free thiol groups, testifying that the 8 cysteine residues in the peptide are displayed, forming 4 disulfide bridges. Circular dichroism spectroscopy showed that camel hepcidin structure was significantly modified at high temperature of 90°C and returns to its original structure when incubation temperature drops back to 20°C. Interestingly, this peptide showed also a greater bactericidal activity, at low concentration of 9.5μM, against E coli, than the synthetic analog DH3. Thus, the production, at a large scale, of the recombinant camel hepcidin, HepcD-His, may be helpful for future therapeutic applications including bacterial infection diseases. Copyright © 2016 John Wiley & Sons, Ltd.

Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Seng, Piseth; Drancourt, Michel; Gouriet, Frédérique; La Scola, Bernard; Fournier, Pierre-Edouard; Rolain, Jean Marc; Raoult, Didier

2009-08-15

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in <1 h using a database comprising > or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.

Early identification of microorganisms in blood culture prior to the detection of a positive signal in the BACTEC FX system using matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

PubMed

Wang, Ming-Cheng; Lin, Wei-Hung; Yan, Jing-Jou; Fang, Hsin-Yi; Kuo, Te-Hui; Tseng, Chin-Chung; Wu, Jiunn-Jong

2015-08-01

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a valuable method for rapid identification of blood stream infection (BSI) pathogens. Integration of MALDI-TOF MS and blood culture system can speed the identification of causative BSI microorganisms. We investigated the minimal microorganism concentrations of common BSI pathogens required for positive blood culture using BACTEC FX and for positive identification using MALDI-TOF MS. The time to detection with positive BACTEC FX and minimal incubation time with positive MALDI-TOF MS identification were determined for earlier identification of common BSI pathogens. The minimal microorganism concentrations required for positive blood culture using BACTEC FX were >10(7)-10(8) colony forming units/mL for most of the BSI pathogens. The minimal microorganism concentrations required for identification using MALDI-TOF MS were > 10(7) colony forming units/mL. Using simulated BSI models, one can obtain enough bacterial concentration from blood culture bottles for successful identification of five common Gram-positive and Gram-negative bacteria using MALDI-TOF MS 1.7-2.3 hours earlier than the usual time to detection in blood culture systems. This study provides an approach to earlier identification of BSI pathogens prior to the detection of a positive signal in the blood culture system using MALDI-TOF MS, compared to current methods. It can speed the time for identification of BSI pathogens and may have benefits of earlier therapy choice and on patient outcome. Copyright © 2013. Published by Elsevier B.V.

Fast implementations of reconstruction-based scatter compensation in fully 3D SPECT image reconstruction

NASA Astrophysics Data System (ADS)

Kadrmas, Dan J.; Frey, Eric C.; Karimi, Seemeen S.; Tsui, Benjamin M. W.

1998-04-01

Accurate scatter compensation in SPECT can be performed by modelling the scatter response function during the reconstruction process. This method is called reconstruction-based scatter compensation (RBSC). It has been shown that RBSC has a number of advantages over other methods of compensating for scatter, but using RBSC for fully 3D compensation has resulted in prohibitively long reconstruction times. In this work we propose two new methods that can be used in conjunction with existing methods to achieve marked reductions in RBSC reconstruction times. The first method, coarse-grid scatter modelling, significantly accelerates the scatter model by exploiting the fact that scatter is dominated by low-frequency information. The second method, intermittent RBSC, further accelerates the reconstruction process by limiting the number of iterations during which scatter is modelled. The fast implementations were evaluated using a Monte Carlo simulated experiment of the 3D MCAT phantom with tracer, and also using experimentally acquired data with tracer. Results indicated that these fast methods can reconstruct, with fully 3D compensation, images very similar to those obtained using standard RBSC methods, and in reconstruction times that are an order of magnitude shorter. Using these methods, fully 3D iterative reconstruction with RBSC can be performed well within the realm of clinically realistic times (under 10 minutes for image reconstruction).

EPE analysis of sub-N10 BEoL flow with and without fully self-aligned via using Coventor SEMulator3D

NASA Astrophysics Data System (ADS)

Franke, Joern-Holger; Gallagher, Matt; Murdoch, Gayle; Halder, Sandip; Juncker, Aurelie; Clark, William

2017-03-01

During the last few decades, the semiconductor industry has been able to scale device performance up while driving costs down. What started off as simple geometrical scaling, driven mostly by advances in lithography, has recently been accompanied by advances in processing techniques and in device architectures. The trend to combine efforts using process technology and lithography is expected to intensify, as further scaling becomes ever more difficult. One promising component of future nodes are "scaling boosters", i.e. processing techniques that enable further scaling. An indispensable component in developing these ever more complex processing techniques is semiconductor process modeling software. Visualization of complex 3D structures in SEMulator3D, along with budget analysis on film thicknesses, CD and etch budgets, allow process integrators to compare flows before any physical wafers are run. Hundreds of "virtual" wafers allow comparison of different processing approaches, along with EUV or DUV patterning options for defined layers and different overlay schemes. This "virtual fabrication" technology produces massively parallel process variation studies that would be highly time-consuming or expensive in experiment. Here, we focus on one particular scaling booster, the fully self-aligned via (FSAV). We compare metal-via-metal (mevia-me) chains with self-aligned and fully-self-aligned via's using a calibrated model for imec's N7 BEoL flow. To model overall variability, 3D Monte Carlo modeling of as many variability sources as possible is critical. We use Coventor SEMulator3D to extract minimum me-me distances and contact areas and show how fully self-aligned vias allow a better me-via distance control and tighter via-me contact area variability compared with the standard self-aligned via (SAV) approach.

Structural confirmation of oligosaccharides newly isolated from sugar beet molasses.

PubMed

Abe, Tatsuya; Horiuchi, Kenichi; Kikuchi, Hiroto; Aritsuka, Tsutomu; Takata, Yusuke; Fukushi, Eri; Fukushi, Yukiharu; Kawabata, Jun; Ueno, Keiji; Onodera, Shuichi; Shiomi, Norio

2012-08-27

Sugar beet molasses is a viscous by-product of the processing of sugar beets into sugar. The molasses is known to contain sucrose and raffinose, a typical trisaccharide, with a well-established structure. Although sugar beet molasses contains various other oligosaccharides as well, the structures of those oligosaccharides have not been examined in detail. The purpose of this study was isolation and structural confirmation of these other oligosaccharides found in sugar beet molasses. Four oligosaccharides were newly isolated from sugar beet molasses using high-performance liquid chromatography (HPLC) and carbon-Celite column chromatography. Structural confirmation of the saccharides was provided by methylation analysis, matrix-assisted laser desorption/ionaization time of flight mass spectrometry (MALDI-TOF-MS), and nuclear magnetic resonance (NMR) measurements. The following oligosaccharides were identified in sugar beet molasses: β-D-galactopyranosyl-(1- > 6)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named β-planteose), α-D-galactopyranosyl-(1- > 1)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named1-planteose), α-D-glucopyranosyl-(1- > 6)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (theanderose), and β-D-glucopyranosyl-(1- > 3)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (laminaribiofructose). 1-planteose and laminaribiofructose were isolated from natural sources for the first time.

A novel fully-humanised 3D skin equivalent to model early melanoma invasion

PubMed Central

Hill, David S; Robinson, Neil D P; Caley, Matthew P; Chen, Mei; O’Toole, Edel A; Armstrong, Jane L; Przyborski, Stefan; Lovat, Penny E

2015-01-01

Metastatic melanoma remains incurable, emphasising the acute need for improved research models to investigate the underlying biological mechanisms mediating tumour invasion and metastasis, and to develop more effective targeted therapies to improve clinical outcome. Available animal models of melanoma do not accurately reflect human disease and current in vitro human skin equivalent models incorporating melanoma cells are not fully representative of the human skin microenvironment. We have developed a robust and reproducible, fully-humanised 3D skin equivalent comprising a stratified, terminally differentiated epidermis and a dermal compartment consisting of fibroblast-generated extracellular matrix. Melanoma cells incorporated into the epidermis were able to invade through the basement membrane and into the dermis, mirroring early tumour invasion in vivo. Comparison of our novel 3D melanoma skin equivalent with melanoma in situ and metastatic melanoma indicates this model accurately recreates features of disease pathology, making it a physiologically representative model of early radial and vertical growth phase melanoma invasion. PMID:26330548

Improvement of attenuation correction in time-of-flight PET/MR imaging with a positron-emitting source.

PubMed

Mollet, Pieter; Keereman, Vincent; Bini, Jason; Izquierdo-Garcia, David; Fayad, Zahi A; Vandenberghe, Stefaan

2014-02-01

Quantitative PET imaging relies on accurate attenuation correction. Recently, there has been growing interest in combining state-of-the-art PET systems with MR imaging in a sequential or fully integrated setup. As CT becomes unavailable for these systems, an alternative approach to the CT-based reconstruction of attenuation coefficients (μ values) at 511 keV must be found. Deriving μ values directly from MR images is difficult because MR signals are related to the proton density and relaxation properties of tissue. Therefore, most research groups focus on segmentation or atlas registration techniques. Although studies have shown that these methods provide viable solutions in particular applications, some major drawbacks limit their use in whole-body PET/MR. Previously, we used an annulus-shaped PET transmission source inside the field of view of a PET scanner to measure attenuation coefficients at 511 keV. In this work, we describe the use of this method in studies of patients with the sequential time-of-flight (TOF) PET/MR scanner installed at the Icahn School of Medicine at Mount Sinai, New York, NY. Five human PET/MR and CT datasets were acquired. The transmission-based attenuation correction method was compared with conventional CT-based attenuation correction and the 3-segment, MR-based attenuation correction available on the TOF PET/MR imaging scanner. The transmission-based method overcame most problems related to the MR-based technique, such as truncation artifacts of the arms, segmentation artifacts in the lungs, and imaging of cortical bone. Additionally, the TOF capabilities of the PET detectors allowed the simultaneous acquisition of transmission and emission data. Compared with the MR-based approach, the transmission-based method provided average improvements in PET quantification of 6.4%, 2.4%, and 18.7% in volumes of interest inside the lung, soft tissue, and bone tissue, respectively. In conclusion, a transmission-based technique with an annulus-shaped transmission source will be more accurate than a conventional MR-based technique for measuring attenuation coefficients at 511 keV in future whole-body PET/MR studies.

Impact of time-of-flight PET on quantification accuracy and lesion detection in simultaneous 18F-choline PET/MRI for prostate cancer.

PubMed

Mühlematter, Urs J; Nagel, Hannes W; Becker, Anton; Mueller, Julian; Vokinger, Kerstin N; de Galiza Barbosa, Felipe; Ter Voert, Edwin E G T; Veit-Haibach, Patrick; Burger, Irene A

2018-05-31

Accurate attenuation correction (AC) is an inherent problem of positron emission tomography magnetic resonance imaging (PET/MRI) systems. Simulation studies showed that time-of-flight (TOF) detectors can reduce PET quantification errors in MRI-based AC. However, its impact on lesion detection in a clinical setting with 18 F-choline has not yet been evaluated. Therefore, we compared TOF and non-TOF 18 F-choline PET for absolute and relative difference in standard uptake values (SUV) and investigated the detection rate of metastases in prostate cancer patients. Non-TOF SUV was significantly lower compared to TOF in all osseous structures, except the skull, in primary lesions of the prostate, and in pelvic nodal and osseous metastasis. Concerning lymph node metastases, both experienced readers detected 16/19 (84%) on TOF PET, whereas on non-TOF PET readers 1 and 2 detected 11 (58%), and 14 (73%), respectively. With TOF PET readers 1 and 2 detected 14/15 (93%) and 11/15 (73%) bone metastases, respectively, whereas detection rate with non-TOF PET was 73% (11/15) for reader 1 and 53% (8/15) for reader 2. The interreader agreement was good for osseous metastasis detection on TOF (kappa 0.636, 95% confidence interval [CI] 0.453-0.810) and moderate on non-TOF (kappa = 0.600, CI 0.438-0.780). TOF reconstruction for 18 F-choline PET/MRI shows higher SUV measurements compared to non-TOF reconstructions in physiological osseous structures as well as pelvic malignancies. Our results suggest that addition of TOF information has a positive impact on lesion detection rate for lymph node and bone metastasis in prostate cancer patients.

Hair analysis of histamine and several metabolites in C3H/HeNCrj mice by ultra performance liquid chromatography with electrospray ionization time-of-flight mass spectrometry (UPLC-ESI-TOF-MS): influence of hair cycle and age.

PubMed

Kawanishi, Hiroki; Toyo'oka, Toshimasa; Ito, Kenichi; Maeda, Munenori; Hamada, Tomoji; Fukushima, Takeshi; Kato, Masaru; Inagaki, Shinsuke

2007-03-01

According to a previous study, the concentration of HA in the hair of SD rats was similar in each rat and the variation in HA concentration was not so great. However, the concentration in human hair was fairly different in each person. As possible reasons for the higher variation in human hair, the differences in hair cycles and age in each person may be considerable. Based on this idea, the studies using C3H/HeNCrj mice who can synchronize their hair cycle were performed for resolution of the influence of hair cycle and age. The effects of hair cycle and age on the concentration of histamine (HA) and several metabolites, i.e., 1-methylhistamine (MHA), imidazole-4-acetic acid (IAA), and 1-methyl-4-imidazole-acetic acid (MIAA), in C3H/HeNCrj mice hair were investigated by ultra-performance liquid chromatography (UPLC) with electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). HA and the metabolites were labeled with 4-(N,N-dimethylaminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (DBD-F) and 4-(N,N-dimethylaminosulfonyl)-7-piperazino-2,1,3-benzoxadiazole (DBD-PZ). The resulting derivatives were separated by UPLC and determined with ESI-TOF-MS. A good linearity was achieved from the calibration curves, obtained by plotting the peak area ratios of the analytes relative to the internal standard (IS), i.e., histamine-alpha,alpha,beta,beta-d4 (HA-d4) or 4-imidazolecarboxylic acid (ICA), against the injected amounts of each compound. The detection limits of HA, MHA, IAA, and MIAA on mass chromatograms were 0.21, 1.0, 0.17, and 0.11 pmol, respectively. The concentrations of HA and the metabolites in the hair shafts and hair root of C3H/HeNCrj mice were determined by this method. The concentration of HA in the hair shaft was relatively higher in the telogen phase. In contrast, the HA content in the anagen phase was increased only in the hair root of old mice. HA appears to possess some effect on hair growth, although the exact reason was not obvious. The HA metabolites, i.e., MHA, MIAA and IAA, were also determined the same as HA; however, the difference in the metabolite concentrations between the hair cycle and age was not clear in both hair shaft and hair root. Such studies of the effect of hair cycle and age on these concentrations are the first report. This analytical technique may be applicable to the determination of various biological compounds in hair.

Magnetic graphene composites as both an adsorbent for sample enrichment and a MALDI-TOF MS matrix for the detection of nitropolycyclic aromatic hydrocarbons in PM2.5.

PubMed

Zhang, Jiangang; Zhang, Li; Li, Ruijin; Hu, Di; Ma, Nengxuan; Shuang, Shaomin; Cai, Zongwei; Dong, Chuan

2015-03-07

A simple and rapid method that uses synthesized magnetic graphene composites as both an adsorbent for enrichment and as a matrix in MALDI-TOF MS analysis was developed for the detection of nitropolycyclic hydrocarbons (nitro-PAHs) in PM2.5 samples. Three nitro-PAHs were detected down to sub pg μL(-1) levels based on calculations from an instrumental signal-to-noise better than 3, which shows the feasibility of using the new materials in MALDI-TOF MS as a potential powerful analytical approach for the analysis of nitro-PAHs in PM2.5 samples.

Quantitative trait loci mapping of the mouse plasma proteome (pQTL).

PubMed

Holdt, Lesca M; von Delft, Annette; Nicolaou, Alexandros; Baumann, Sven; Kostrzewa, Markus; Thiery, Joachim; Teupser, Daniel

2013-02-01

A current challenge in the era of genome-wide studies is to determine the responsible genes and mechanisms underlying newly identified loci. Screening of the plasma proteome by high-throughput mass spectrometry (MALDI-TOF MS) is considered a promising approach for identification of metabolic and disease processes. Therefore, plasma proteome screening might be particularly useful for identifying responsible genes when combined with analysis of variation in the genome. Here, we describe a proteomic quantitative trait locus (pQTL) study of plasma proteome screens in an F(2) intercross of 455 mice mapped with 177 genetic markers across the genome. A total of 69 of 176 peptides revealed significant LOD scores (≥5.35) demonstrating strong genetic regulation of distinct components of the plasma proteome. Analyses were confirmed by mechanistic studies and MALDI-TOF/TOF, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of the two strongest pQTLs: A pQTL for mass-to-charge ratio (m/z) 3494 (LOD 24.9, D11Mit151) was identified as the N-terminal 35 amino acids of hemoglobin subunit A (Hba) and caused by genetic variation in Hba. Another pQTL for m/z 8713 (LOD 36.4; D1Mit111) was caused by variation in apolipoprotein A2 (Apoa2) and cosegregated with HDL cholesterol. Taken together, we show that genome-wide plasma proteome profiling in combination with genome-wide genetic screening aids in the identification of causal genetic variants affecting abundance of plasma proteins.

Quantitative Trait Loci Mapping of the Mouse Plasma Proteome (pQTL)

PubMed Central

Holdt, Lesca M.; von Delft, Annette; Nicolaou, Alexandros; Baumann, Sven; Kostrzewa, Markus; Thiery, Joachim; Teupser, Daniel

2013-01-01

A current challenge in the era of genome-wide studies is to determine the responsible genes and mechanisms underlying newly identified loci. Screening of the plasma proteome by high-throughput mass spectrometry (MALDI-TOF MS) is considered a promising approach for identification of metabolic and disease processes. Therefore, plasma proteome screening might be particularly useful for identifying responsible genes when combined with analysis of variation in the genome. Here, we describe a proteomic quantitative trait locus (pQTL) study of plasma proteome screens in an F2 intercross of 455 mice mapped with 177 genetic markers across the genome. A total of 69 of 176 peptides revealed significant LOD scores (≥5.35) demonstrating strong genetic regulation of distinct components of the plasma proteome. Analyses were confirmed by mechanistic studies and MALDI-TOF/TOF, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of the two strongest pQTLs: A pQTL for mass-to-charge ratio (m/z) 3494 (LOD 24.9, D11Mit151) was identified as the N-terminal 35 amino acids of hemoglobin subunit A (Hba) and caused by genetic variation in Hba. Another pQTL for m/z 8713 (LOD 36.4; D1Mit111) was caused by variation in apolipoprotein A2 (Apoa2) and cosegregated with HDL cholesterol. Taken together, we show that genome-wide plasma proteome profiling in combination with genome-wide genetic screening aids in the identification of causal genetic variants affecting abundance of plasma proteins. PMID:23172855

A novel method for modeling the neutron time of flight (nTOF) detector response in current mode to inertial confinement fusion experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Alan J.; Cooper, Gary Wayne; Ruiz, Carlos L.

2013-09-01

There are several machines in this country that produce short bursts of neutrons for various applications. A few examples are the Zmachine, operated by Sandia National Laboratories in Albuquerque, NM; the OMEGA Laser Facility at the University of Rochester in Rochester, NY; and the National Ignition Facility (NIF) operated by the Department of Energy at Lawrence Livermore National Laboratory in Livermore, California. They all incorporate neutron time of flight (nTOF) detectors which measure neutron yield, and the shapes of the waveforms from these detectors contain germane information about the plasma conditions that produce the neutrons. However, the signals can alsomore » be %E2%80%9Cclouded%E2%80%9D by a certain fraction of neutrons that scatter off structural components and also arrive at the detectors, thereby making analysis of the plasma conditions more difficult. These detectors operate in current mode - i.e., they have no discrimination, and all the photomultiplier anode charges are integrated rather than counted individually as they are in single event counting. Up to now, there has not been a method for modeling an nTOF detector operating in current mode. MCNPPoliMiwas developed in 2002 to simulate neutron and gammaray detection in a plastic scintillator, which produces a collision data output table about each neutron and photon interaction occurring within the scintillator; however, the postprocessing code which accompanies MCNPPoliMi assumes a detector operating in singleevent counting mode and not current mode. Therefore, the idea for this work had been born: could a new postprocessing code be written to simulate an nTOF detector operating in current mode? And if so, could this process be used to address such issues as the impact of neutron scattering on the primary signal? Also, could it possibly even identify sources of scattering (i.e., structural materials) that could be removed or modified to produce %E2%80%9Ccleaner%E2%80%9D neutron signals? This process was first developed and then applied to the axial neutron time of flight detectors at the ZFacility mentioned above. First, MCNPPoliMi was used to model relevant portions of the facility between the source and the detector locations. To obtain useful statistics, variance reduction was utilized. Then, the resulting collision output table produced by MCNPPoliMi was further analyzed by a MATLAB postprocessing code. This converted the energy deposited by neutron and photon interactions in the plastic scintillator (i.e., nTOF detector) into light output, in units of MeVee%D1%84 (electron equivalent) vs time. The time response of the detector was then folded into the signal via another MATLAB code. The simulated response was then compared with experimental data and shown to be in good agreement. To address the issue of neutron scattering, an %E2%80%9CIdeal Case,%E2%80%9D (i.e., a plastic scintillator was placed at the same distance from the source for each detector location) with no structural components in the problem. This was done to produce as %E2%80%9Cpure%E2%80%9D a neutron signal as possible. The simulated waveform from this %E2%80%9CIdeal Case%E2%80%9D was then compared with the simulated data from the %E2%80%9CFull Scale%E2%80%9D geometry (i.e., the detector at the same location, but with all the structural materials now included). The %E2%80%9CIdeal Case%E2%80%9D was subtracted from the %E2%80%9CFull Scale%E2%80%9D geometry case, and this was determined to be the contribution due to scattering. The time response was deconvolved out of the empirical data, and the contribution due to scattering was then subtracted out of it. A transformation was then made from dN/dt to dN/dE to obtain neutron spectra at two different detector locations.« less

Metabonomic analysis of urine from rats after low-dose exposure to 3-chloro-1,2-propanediol using UPLC-MS.

PubMed

Liu, Liyan; He, Yujie; Lu, Huimin; Wang, Maoqing; Sun, Changhao; Na, Lixin; Li, Ying

2013-05-15

To study the toxic effect of chronic exposure to 3-chloro-1,2-propanediol (3-MCPD) at low doses, a metabonomics approach based on ultrahigh-performance liquid chromatography and quadruple time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was performed. Two different doses of 3-MCPD (1.1 and 5.5mg/kg bw/d) were administered to Wistar rats for 120 days (1.1mg/kg bw/d: lowest observed adverse effect level [LOAEL]). The metabolite profiles and biochemical parameters were obtained at five time points after treatment. For the 3-MCPD-treated groups, a significant change in urinary N-acetyl-β-d-glucosaminidase and β-d-galactosidase was detected on day 90, while some biomarkers based on the metabonomics, such as N-acetylneuraminic acid, N-acetyl-l-tyrosine, and gulonic acid, were detected on day 30. These results suggest that these biomarkers changed more sensitively and earlier than conventional biochemical parameters and were thus considered early and sensitive biomarkers of exposure to 3-MCPD; these biomarkers provide more information on toxicity than conventional biochemical parameters. These results might be helpful to investigate the toxic mechanisms of 3-MCPD and provide a scientific basis for assessing the effect of chronic exposure to low-dose 3-MCPD on human health. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

A rapid diagnostic workflow for cefotaxime-resistant Escherichia coli and Klebsiella pneumoniae detection from blood cultures by MALDI-TOF mass spectrometry.

PubMed

De Carolis, Elena; Paoletti, Silvia; Nagel, Domenico; Vella, Antonietta; Mello, Enrica; Palucci, Ivana; De Angelis, Giulia; D'Inzeo, Tiziana; Sanguinetti, Maurizio; Posteraro, Brunella; Spanu, Teresa

2017-01-01

Nowadays, the global spread of resistance to oxyimino-cephalosporins in Enterobacteriaceae implies the need for novel diagnostics that can rapidly target resistant organisms from these bacterial species. In this study, we developed and evaluated a Direct Mass Spectrometry assay for Beta-Lactamase (D-MSBL) that allows direct identification of (oxyimino)cephalosporin-resistant Escherichia coli or Klebsiella pneumoniae from positive blood cultures (BCs), by using the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technology. The D-MSBL assay was performed on 93 E. coli or K. pneumoniae growing BC samples that were shortly co-incubated with cefotaxime (CTX) as the indicator cephalosporin. Susceptibility and resistance defining peaks from the samples' mass spectra were analyzed by a novel algorithm for bacterial organism classification. The D-MSBL assay allowed discrimination between E. coli and K. pneumoniae that were resistant or susceptible to CTX with a sensitivity of 86.8% and a specificity of 98.2%. The proposed algorithm-based D-MSBL assay, if integrated in the routine laboratory diagnostic workflow, may be useful to enhance the establishment of appropriate antibiotic therapy and to control the threat of oxyimino-cephalosporin resistance in hospital.

Combined mass spectrometry-based metabolite profiling of different pigmented rice (Oryza sativa L.) seeds and correlation with antioxidant activities.

PubMed

Kim, Ga Ryun; Jung, Eun Sung; Lee, Sarah; Lim, Sun-Hyung; Ha, Sun-Hwa; Lee, Choong Hwan

2014-09-29

Nine varieties of pigmented rice (Oryza sativa L.) seeds that were black, red, or white were used to perform metabolite profiling by using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and gas chromatography (GC) TOF-MS, to measure antioxidant activities. Clear grouping patterns determined by the color of the rice seeds were identified in principle component analysis (PCA) derived from UPLC-Q-TOF-MS. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimer, proanthocyanidin trimer, apigenin-6-C-glugosyl-8-C-arabiboside, tricin-O-rhamnoside-O-hexoside, and lipids were identified as significantly different secondary metabolites. In PCA score plots derived from GC-TOF-MS, Jakwangdo (JKD) and Ilpoom (IP) species were discriminated from the other rice seeds by PC1 and PC2. Valine, phenylalanine, adenosine, pyruvate, nicotinic acid, succinic acid, maleic acid, malonic acid, gluconic acid, xylose, fructose, glucose, maltose, and myo-inositol were significantly different primary metabolites in JKD species, while GABA, asparagine, xylitol, and sucrose were significantly distributed in IP species. Analysis of antioxidant activities revealed that black and red rice seeds had higher activity than white rice seeds. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimers, proanthocyanidin trimers, and catechin were highly correlated with antioxidant activities, and were more plentiful in black and red rice seeds. These results are expected to provide valuable information that could help improve and develop rice-breeding techniques.

Oral Mucosal Injection of a Local Anesthetic Solution Containing Epinephrine Enhances Muscle Relaxant Effects of Rocuronium

PubMed Central

Ninomiya, Asako; Terakawa, Yui; Matsuura, Nobuyuki; Ichinohe, Tatsuya; Kaneko, Yuzuru

2012-01-01

The purpose of this study was to examine how submucosal injection of a clinically relevant dose of a lidocaine hydrochloride solution containing epinephrine affects the muscle relaxant effects of rocuronium bromide. Sixteen patients scheduled for orthognathic surgery participated in this study. All patients were induced with fentanyl citrate, a target-controlled infusion of propofol and rocuronium bromide. Anesthesia was maintained by total intravenous anesthesia. After nasotracheal intubation, an infusion of rocuronium bromide was started at 7 µg/kg/min, and the infusion rate was then adjusted to maintain a train of four (TOF) ratio at 10 to 15%. The TOF ratio just prior to oral mucosal injection of a 1% lidocaine hydrochloride solution containing 10 µg/mL epinephrine (LE) was taken as the baseline. TOF ratio was observed for 20 minutes, with 1-minute intervals following the start of injection. Mean epinephrine dose was 85.6 ± 18.6 µg and mean infusion rate of rocuronium bromide was 6.3 ± 1.6 µg/kg/min. TOF ratio began to decrease 2 minutes after the injection of LE, reached the minimum value at 3.1 ± 3.6% 12 minutes after the injection, and then began to recover. We conclude that oral mucosal injection of LE enhances the muscle relaxant effects of rocuronium bromide. PMID:22428970

APD Response Time Measurements for Future TOF-E Systems

NASA Astrophysics Data System (ADS)

Starkey, M. J.; Ogasawara, K.; Dayeh, M. A.; Desai, M. I.

2017-12-01

In space physics, the ability to detect ions is crucial to understanding plasma distributions in the solar wind. This usually typically requires the determination of the particle's mass, charge, and total energy. Current ion detection schemes are implemented in three sequential parts; an electrostatic analyzer for energy per charge (E/Q) measurements, a time-of-flight (TOF) for mass per charge (M/Q) measurements, and a solid-state detector (SSD) for total energy (E) measurements. Recent work has suggested the use of avalanche photodiode detectors (APD) for a simultaneous TOF and total energy (TOF-E) measurement system, which would replace traditional SSDs, simplify design, and reduce costs. Although TOF based ion spectrometry typically requires timing resolution of <1ns, the timing profile for ion detection by APDs is not well understood. In this study we examine the timing profile of 3 different APDs for ion measurements over a suprathermal energy range of 50-300 keV. The three APDs differ by their doping type (N or P) and their detector thickness (30 μm or 150 μm). We find that APD P30, which is P doped and 30μm thick, provides the fastest rise times of the three APDs. Furthermore, these rise times are species independent and less than 1 ns. Our study shows that APDs are capable of sub-nanosecond response times for low energy ions and thus supports the future use of APDs in replacing SSDs in some TOF-E systems.

Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry

USDA-ARS?s Scientific Manuscript database

Portions of this work were presented earlier as an oral presentation on June 2nd 2009 at the 57th American Society of Mass Spectrometry Conference (May 31-June 4, 2009, Philadelphia, PA). We report covalent attachment via a thiol ester linkage of 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid...

Direct analysis and identification of pathogenic Lichtheimia species by matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry.

PubMed

Schrödl, Wieland; Heydel, Tilo; Schwartze, Volker U; Hoffmann, Kerstin; Grosse-Herrenthey, Anke; Walther, Grit; Alastruey-Izquierdo, Ana; Rodriguez-Tudela, Juan Luis; Olias, Philipp; Jacobsen, Ilse D; de Hoog, G Sybren; Voigt, Kerstin

2012-02-01

Zygomycetes of the order Mucorales can cause life-threatening infections in humans. These mucormycoses are emerging and associated with a rapid tissue destruction and high mortality. The resistance of Mucorales to antimycotic substances varies between and within clinically important genera such as Mucor, Rhizopus, and Lichtheimia. Thus, an accurate diagnosis before onset of antimycotic therapy is recommended. Matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) is a potentially powerful tool to rapidly identify infectious agents on the species level. We investigated the potential of MALDI-TOF MS to differentiate Lichtheimia species, one of the most important agents of mucormycoses. Using the Bruker Daltonics FlexAnalysis (version 3.0) software package, a spectral database library with m/z ratios of 2,000 to 20,000 Da was created for 19 type and reference strains of clinically relevant Zygomycetes of the order Mucorales (12 species in 7 genera). The database was tested for accuracy by use of 34 clinical and environmental isolates of Lichtheimia comprising a total of five species. Our data demonstrate that MALDI-TOF MS can be used to clearly discriminate Lichtheimia species from other pathogenic species of the Mucorales. Furthermore, the method is suitable to discriminate species within the genus. The reliability and robustness of the MALDI-TOF-based identification are evidenced by high score values (above 2.3) for the designation to a certain species and by moderate score values (below 2.0) for the discrimination between clinically relevant (Lichtheimia corymbifera, L. ramosa, and L. ornata) and irrelevant (L. hyalospora and L. sphaerocystis) species. In total, all 34 strains were unequivocally identified by MALDI-TOF MS with score values of >1.8 down to the generic level, 32 out of 34 of the Lichtheimia isolates (except CNM-CM 5399 and FSU 10566) were identified accurately with score values of >2 (probable species identification), and 25 of 34 isolates were identified to the species level with score values of >2.3 (highly probable species identification). The MALDI-TOF MS-based method reported here was found to be reproducible and accurate, with low consumable costs and minimal preparation time.

Gram-stain plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry) for a rapid diagnosis of urinary tract infection.

PubMed

Burillo, Almudena; Rodríguez-Sánchez, Belén; Ramiro, Ana; Cercenado, Emilia; Rodríguez-Créixems, Marta; Bouza, Emilio

2014-01-01

Microbiological confirmation of a urinary tract infection (UTI) takes 24-48 h. In the meantime, patients are usually given empirical antibiotics, sometimes inappropriately. We assessed the feasibility of sequentially performing a Gram stain and MALDI-TOF MS mass spectrometry (MS) on urine samples to anticipate clinically useful information. In May-June 2012, we randomly selected 1000 urine samples from patients with suspected UTI. All were Gram stained and those yielding bacteria of a single morphotype were processed for MALDI-TOF MS. Our sequential algorithm was correlated with the standard semiquantitative urine culture result as follows: Match, the information provided was anticipative of culture result; Minor error, the information provided was partially anticipative of culture result; Major error, the information provided was incorrect, potentially leading to inappropriate changes in antimicrobial therapy. A positive culture was obtained in 242/1000 samples. The Gram stain revealed a single morphotype in 207 samples, which were subjected to MALDI-TOF MS. The diagnostic performance of the Gram stain was: sensitivity (Se) 81.3%, specificity (Sp) 93.2%, positive predictive value (PPV) 81.3%, negative predictive value (NPV) 93.2%, positive likelihood ratio (+LR) 11.91, negative likelihood ratio (-LR) 0.20 and accuracy 90.0% while that of MALDI-TOF MS was: Se 79.2%, Sp 73.5, +LR 2.99, -LR 0.28 and accuracy 78.3%. The use of both techniques provided information anticipative of the culture result in 82.7% of cases, information with minor errors in 13.4% and information with major errors in 3.9%. Results were available within 1 h. Our serial algorithm provided information that was consistent or showed minor errors for 96.1% of urine samples from patients with suspected UTI. The clinical impacts of this rapid UTI diagnosis strategy need to be assessed through indicators of adequacy of treatment such as a reduced time to appropriate empirical treatment or earlier withdrawal of unnecessary antibiotics.

Daily chronomics of proteomic profile in aging and rotenone-induced Parkinson's disease model in male Wistar rat and its modulation by melatonin.

PubMed

Jagota, Anita; Mattam, Ushodaya

2017-08-01

Aging is associated with changes in several basic parameters of circadian timing system (CTS) in mammals leading to circadian dysfunction. We had reported earlier that upon aging and in rotenone induced Parkinson's disease (RIPD) rat model there were significant alterations in the core clock genes expression levels and daily pulses. To identify biomarkers of aging and PD chronomics of proteomic day-night profiles in suprachiasmatic nucleus (SCN), pineal and substantia nigra (SN) in 3 month (m), 12, 24 m and RIPD rat model were studied at two time points i.e. Zeitgeber Time (ZT)-6 (mid-day) and ZT-18 (mid-night). Proteome analysis was done by using two dimensional (2-D) electrophoresis and the spots showing robust day-night variations were identified by using MALDI TOF/TOF analysis. In 3 m rats the number of proteins showing day-night variations were relatively more than 12, 24 m and RIPD rat model in SCN and SN. But in pineal there was increase in number of protein spots showing day-night variations in 24 m. Mass spectroscopy of the protein spots showing robust day night variation in aging and RIPD rats were identified. As melatonin, a multitasking molecule, an endogenous synchronizer of rhythm, an antioxidant and an antiaging drug, declines with aging, the effects of melatonin administration on differential alterations in chronomics of 2-D protein profiles in aging and RIPD male Wistar rats were studied. We report here that the melatonin could be playing an important role in modulating the chronomics of 2-D protein profiles. Additionally, various proteins were identified for the first time in this study showing significant day night variation in SCN, pineal and SN may prove useful towards targeting novel treatments for circadian dysfunction, good health and longevity.

MDN-0170, a New Napyradiomycin from Streptomyces sp. Strain CA-271078

PubMed Central

Lacret, Rodney; Pérez-Victoria, Ignacio; Oves-Costales, Daniel; de la Cruz, Mercedes; Domingo, Elizabeth; Martín, Jesús; Díaz, Caridad; Vicente, Francisca; Genilloud, Olga; Reyes, Fernando

2016-01-01

A new napyradiomycin, MDN-0170 (1), was isolated from the culture broth of the marine-derived actinomycete strain CA-271078, together with three known related compounds identified as 4-dehydro-4a-dechloronapyradiomycin A1 (2), napyradiomycin A1 (3) and 3-chloro-6,8-dihydroxy-8-α-lapachone (4). The structure of the new compound was determined using a combination of spectroscopic techniques, including 1D and 2D NMR and electrospray-time of flight mass spectrometry (ESI-TOF MS). The relative configuration of compound 1, which contains two independent stereoclusters, has been established by molecular modelling in combination with nOe and coupling constant analyses. Biosynthetic arguments also allowed us to propose its absolute stereochemistry. The antimicrobial properties of the compounds isolated were evaluated against methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, Aspergillus fumigatus, and Candida albicans. The potent bioactivity previously reported for compounds 2 and 3 against methicillin-sensitive S. aureus has been extended to methicillin-resistant strains in this report. PMID:27763545

Multi-spectroscopic analysis of cholesterol gallstone using TOF-SIMS, FTIR and UV-Vis spectroscopy

NASA Astrophysics Data System (ADS)

Jaswal, Brij Bir S.; Kumar, Vinay; Swart, H. C.; Sharma, Jitendra; Rai, Pradeep K.; Singh, Vivek K.

2015-10-01

For the first time, spatial distribution of major and trace elements has been studied in cholesterol gallstones using time-of-flight secondary mass ion mass spectrometry (TOF-SIMS). The TOF-SIMS has been used to study the elemental constituents of the center and surface parts of the gallstone sample. We have classified the gallstone sample using Fourier transform spectroscopy. The detected elements in cholesterol gallstone sample were carbon (C), hydrogen (H), calcium (Ca), sodium (Na), potassium (K), strontium (Sr), copper (Cu), iron (Fe), chromium (Cr), mercury (Hg) and lead (Pb). The detected molecules in the cholesterol gallstone were CH3 +, CO3 +, CaCO3 + and C3H+. Our results revealed that the contents of these elements in cholesterol gallstone were higher in the center part than that in the surface part. In the present paper, we have also presented the UV-Vis spectroscopic studies of the center and surface parts of the gallstone sample which indicated the presence of a higher content of cholesterol in the surface part and bilirubin in the center part.

Profiling LC-DAD-ESI-TOF MS method for the determination of phenolic metabolites from avocado (Persea americana).

PubMed

Hurtado-Fernández, Elena; Carrasco-Pancorbo, Alegría; Fernández-Gutiérrez, Alberto

2011-03-23

A powerful HPLC-DAD-ESI-TOF MS method was established for the efficient identification of the chemical constituents in the methanolic extracts of avocado (Persea americana). Separation and detection conditions were optimized by using a standard mix containing 39 compounds belonging to phenolic acids and different categories of flavonoids, analytes that could be potentially present in the avocado extracts. Optimum LC separation was achieved on a Zorbax Eclipse Plus C18 analytical column (4.6×150 mm, 1.8 μm particle size) by gradient elution with water+acetic acid (0.5%) and acetonitrile as mobile phases, at a flow rate of 1.6 mL/min. The detection was carried out by ultraviolet-visible absorption and ESI-TOF MS. The developed method was applied to the study of 3 different varieties of avocado, and 17 compounds were unequivocally identified with standards. Moreover, around 25 analytes were tentatively identified by taking into account the accuracy and isotopic information provided by TOF MS.

Can acceleromyography detect low levels of residual paralysis? A probability approach to detect a mechanomyographic train-of-four ratio of 0.9.

PubMed

Capron, Florent; Alla, Francois; Hottier, Claire; Meistelman, Claude; Fuchs-Buder, Thomas

2004-05-01

The incidence of residual paralysis, i.e., a mechanomyographic train-of-four (TOF) ratio (T4/T1) less than 0.9, remains frequent. Routine acceleromyography has been proposed to detect residual paralysis in clinical practice. Although acceleromyographic data are easy to obtain, they differ from mechanomyographic data, with which they are not interchangeable. The current study aimed to determine (1) the acceleromyographic TOF ratio that detects residual paralysis with a 95% probability, and (2) the impact of calibration and normalization on this predictive acceleromyographic value. In 60 patients, recovery from neuromuscular block was assessed simultaneously with mechanomyography and acceleromyography. To obtain calibrated acceleromyographic TOF ratios in group A, the implemented calibration modus 2 was activated in the TOF-Watch S; to obtain uncalibrated acceleromyographic TOF ratios in group B, the current was manually set at 50 mA (n = 30 for each). In addition, data in group B were normalized (i.e., dividing the final TOF ratio by the baseline value). The agreement between mechanomyography and acceleromyography was assessed by calculating the intraclass correlation coefficient. Negative predictive values were calculated for detecting residual paralysis from acceleromyographic TOFs of 0.9, 0.95, and 1.0. : For a mechanomyographic TOF of 0.9 or greater, the corresponding acceleromyographic TOF was 0.95 (range, 0.86-1.0), and the negative predictive values for acceleromyographic TOFs of 0.9, 0.95, and 1.0 were 37% (95% CI, 20-56%), 70% (95% CI, 51-85%), and 97% (95% CI, 83-100%), respectively. Group B: Without normalization, an acceleromyographic TOF of 0.97 (range, 0.68-1.18) corresponded to a mechanomyographic TOF of 0.9 or greater, with negative predictive values for acceleromyographic TOFs of 0.9, 0.95, and 1.0 being 40% (95% CI, 23-59%), 60% (95% CI, 41-77%), and 77% (95% CI, 58-90%), respectively. After normalization, an acceleromyographic TOF of 0.89 (range, 0.63-1.06) corresponded to a mechanomyographic TOF of 0.9 or greater, and the negative predictive values of acceleromyographic TOFs of 0.9, 0.95, and 1.0 were 89% (95% CI, 70-98%), 92% (95% CI, 75-99%), and 96% (95% CI, 80-100%), respectively. To exclude residual paralysis reliably when using acceleromyography, TOF recovery to 1.0 is mandatory.

High-Precision Simulation of the Gravity Field of Rapidly-Rotating Barotropes in Hydrostatic Equilibrium

NASA Astrophysics Data System (ADS)

Hubbard, W. B.

2013-12-01

The so-called theory of figures (TOF) uses potential theory to solve for the structure of highly distorted rotating liquid planets in hydrostatic equilibrium. TOF is noteworthy both for its antiquity (Maclaurin 1742) and its mathematical complexity. Planned high-precision gravity measurements near the surfaces of Jupiter and Saturn (possibly detecting signals ~ microgal) will place unprecedented requirements on TOF, not because one expects hydrostatic equilibrium to that level, but because nonhydrostatic components in the surface gravity, at expected levels ~ 1 milligal, must be referenced to precise hydrostatic-equilibrium models. The Maclaurin spheroid is both a useful test of numerical TOF codes (Hubbard 2012, ApJ Lett 756:L15), and an approach to an efficient TOF code for arbitrary barotropes of variable density (Hubbard 2013, ApJ 768:43). For the latter, one trades off vertical resolution by replacing a continuous barotropic pressure-density relation with a stairstep relation, corresponding to N concentric Maclaurin spheroids (CMS), each of constant density. The benefit of this trade-off is that two-dimensional integrals over the mass distributions at each interface are reduced to one-dimensional integrals, quickly and accurately evaluated by Gaussian quadrature. The shapes of the spheroids comprise N level surfaces within the planet and at its surface, are gravitationally coupled to each other, and are found by self-consistent iteration, relaxing to a final configuration to within the computer's precision limits. The angular and radial variation of external gravity (using the usual geophysical expansion in multipole moments) can be found to the limit of typical floating point precision (~ 1.e-14), much better than the expected noise/signal for either the Juno or Cassini gravity experiments. The stairstep barotrope can be adjusted to fit a prescribed continuous or discontinuous interior barotrope, and can be made to approximate it to any required precision by increasing N. One can insert a higher density of CMSs toward the surface of an interior model in order to more accurately model high-order gravitational moments. The magnitude of high-order moments predicted by TOF declines geometrically with order number, and falls below the magnitude of expected non-hydrostatic terms produced by interior dynamics at ~ order 10 and above. Juno's sensitivity is enough to detect tidal gravity signals from Galilean satellites. The CMS method can be generalized to predict tidal zonal and tesseral terms consistent with an interior model fitted to measured zonal harmonics. For this purpose, two-dimensional Gaussian quadrature is necessary at each CMS interface. However, once the model is relaxed to equilibrium, one need not refit the model to the average zonal harmonics because of the smallness of the tidal terms. I will describe how the CMS method has been validated through comparisons with standard TOF models for which fully or partially analytic solutions exist, as well as through consistency checks. At this stage in software development in preparation for Jupiter orbit, we are focused on increasing the speed of the code in order to more efficiently search the parameter space of acceptable Jupiter interior models, as well as to interface it with advanced hydrogen-helium equations of state.

Imaging and Rapid-Scanning Ion Mass Spectrometer (IRM) for the CASSIOPE e-POP Mission

NASA Astrophysics Data System (ADS)

Yau, Andrew W.; Howarth, Andrew; White, Andrew; Enno, Greg; Amerl, Peter

2015-06-01

The imaging and rapid-scanning ion mass spectrometer (IRM) is part of the Enhanced Polar Outflow Probe (e-POP) instrument suite on the Canadian CASSIOPE small satellite. Designed to measure the composition and detailed velocity distributions of ions in the ˜1-100 eV/q range on a non-spinning spacecraft, the IRM sensor consists of a planar entrance aperture, a pair of electrostatic deflectors, a time-of-flight (TOF) gate, a hemispherical electrostatic analyzer, and a micro-channel plate (MCP) detector. The TOF gate measures the transit time of each detected ion inside the sensor. The hemispherical analyzer disperses incident ions by their energy-per-charge and azimuth in the aperture plane onto the detector. The two electrostatic deflectors may be optionally programmed to step through a sequence of deflector voltages, to deflect ions of different incident elevation out of the aperture plane and energy-per-charge into the sensor aperture for sampling. The position and time of arrival of each detected ion at the detector are measured, to produce an image of 2-dimensional (2D), mass-resolved ion velocity distribution up to 100 times per second, or to construct a composite 3D velocity distribution by combining successive images in a deflector voltage sequence. The measured distributions are then used to investigate ion composition, density, drift velocity and temperature in polar ion outflows and related acceleration and transport processes in the topside ionosphere.

Proteins altered by elevated levels of palmitate or glucose implicated in impaired glucose-stimulated insulin secretion

PubMed Central

Sol, E-ri M; Hovsepyan, Meri; Bergsten, Peter

2009-01-01

Background Development of type 2 diabetes mellitus (T2DM) is characterized by aberrant insulin secretory patterns, where elevated insulin levels at non-stimulatory basal conditions and reduced hormonal levels at stimulatory conditions are major components. To delineate mechanisms responsible for these alterations we cultured INS-1E cells for 48 hours at 20 mM glucose in absence or presence of 0.5 mM palmitate, when stimulatory secretion of insulin was reduced or basal secretion was elevated, respectively. Results After culture, cells were protein profiled by SELDI-TOF-MS and 2D-PAGE. Differentially expressed proteins were discovered and identified by peptide mass fingerprinting. Complimentary protein profiles were obtained by the two approaches with SELDI-TOF-MS being more efficient in separating proteins in the low molecular range and 2D-PAGE in the high molecular range. Identified proteins included alpha glucosidase, calmodulin, gars, glucose-6-phosphate dehydrogenase, heterogenous nuclear ribonucleoprotein A3, lon peptidase, nicotineamide adenine dinucleotide hydrogen (NADH) dehydrogenase, phosphoglycerate kinase, proteasome p45, rab2, pyruvate kinase and t-complex protein. The observed glucose-induced differential protein expression pattern indicates enhanced glucose metabolism, defense against reactive oxygen species, enhanced protein translation, folding and degradation and decreased insulin granular formation and trafficking. Palmitate-induced changes could be related to altered exocytosis. Conclusion The identified altered proteins indicate mechanism important for altered β-cell function in T2DM. PMID:19607692

Rapid identification of microorganisms from positive blood cultures by MALDI-TOF mass spectrometry subsequent to very short-term incubation on solid medium.

PubMed

Idelevich, E A; Schüle, I; Grünastel, B; Wüllenweber, J; Peters, G; Becker, K

2014-10-01

Rapid identification of the causative microorganism is important for appropriate antimicrobial therapy of bloodstream infections. Bacteria from positive blood culture (BC) bottles are not readily available for identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Lysis and centrifugation procedures suggested for direct MALDI-TOF MS from positive BCs without previous culture are associated with additional hands-on processing time and costs. Here, we describe an alternative approach applying MALDI-TOF MS from bacterial cultures incubated very briefly on solid medium. After plating of positive BC broth on Columbia blood agar (n = 165), MALDI-TOF MS was performed after 1.5, 2, 3, 4, 5, 6, 7, 8, 12 and (for control) 24 h of incubation until reliable identification to the species level was achieved (score ≥2.0). Mean incubation time needed to achieve species-level identification was 5.9 and 2.0 h for Gram-positive aerobic cocci (GPC, n = 86) and Gram-negative aerobic rods (GNR, n = 42), respectively. Short agar cultures with incubation times ≤2, ≤4, ≤6, ≤8 and ≤12 h yielded species identification in 1.2%, 18.6%, 64.0%, 96.5%, 98.8% of GPC, and in 76.2%, 95.2%, 97.6%, 97.6%, 97.6% of GNR, respectively. Control species identification at 24 h was achieved in 100% of GPC and 97.6% of GNR. Ethanol/formic acid protein extraction performed for an additional 34 GPC isolates cultivated from positive BCs showed further reduction in time to species identification (3.1 h). MALDI-TOF MS using biomass subsequent to very short-term incubation on solid medium allows very early and reliable bacterial identification from positive BCs without additional time and cost expenditure. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

An orientation analysis method for protein immobilized on quantum dot particles

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Inoue, Masae

2009-11-01

The evaluation of orientation of biomolecules immobilized on nanodevices is crucial for the development of high performance devices. Such analysis requires ultra high sensitivity so as to be able to detect less than one molecular layer on a device. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has sufficient sensitivity to evaluate the uppermost surface structure of a single molecular layer. The objective of this study is to develop an orientation analysis method for proteins immobilized on nanomaterials such as quantum dot particles, and to evaluate the orientation of streptavidin immobilized on quantum dot particles by means of TOF-SIMS. In order to detect fragment ions specific to the protein surface, a monoatomic primary ion source (Ga +) and a cluster ion source (Au 3+) were employed. Streptavidin-immobilized quantum dot particles were immobilized on aminosilanized ITO glass plates at amino groups by covalent bonding. The reference samples streptavidin directly immobilized on ITO plates were also prepared. All samples were dried with a freeze dryer before TOF-SIMS measurement. The positive secondary ion spectra of each sample were obtained using TOF-SIMS with Ga + and Au 3+, respectively, and then they were compared so as to characterize each sample and detect the surface structure of the streptavidin immobilized with the biotin-immobilized quantum dots. The chemical structures of the upper surface of the streptavidin molecules immobilized on the quantum dot particles were evaluated with TOF-SIMS spectra analysis. The indicated surface side of the streptavidin molecules immobilized on the quantum dots includes the biotin binding site.

Multisensory System for Fruit Harvesting Robots. Experimental Testing in Natural Scenarios and with Different Kinds of Crops

PubMed Central

Fernández, Roemi; Salinas, Carlota; Montes, Héctor; Sarria, Javier

2014-01-01

The motivation of this research was to explore the feasibility of detecting and locating fruits from different kinds of crops in natural scenarios. To this end, a unique, modular and easily adaptable multisensory system and a set of associated pre-processing algorithms are proposed. The offered multisensory rig combines a high resolution colour camera and a multispectral system for the detection of fruits, as well as for the discrimination of the different elements of the plants, and a Time-Of-Flight (TOF) camera that provides fast acquisition of distances enabling the localisation of the targets in the coordinate space. A controlled lighting system completes the set-up, increasing its flexibility for being used in different working conditions. The pre-processing algorithms designed for the proposed multisensory system include a pixel-based classification algorithm that labels areas of interest that belong to fruits and a registration algorithm that combines the results of the aforementioned classification algorithm with the data provided by the TOF camera for the 3D reconstruction of the desired regions. Several experimental tests have been carried out in outdoors conditions in order to validate the capabilities of the proposed system. PMID:25615730

Low energy positron beam system for the investigation of 2D and porous materials

NASA Astrophysics Data System (ADS)

Chrysler, M. D.; Chirayath, V. A.; Mcdonald, A. D.; Gladen, R. W.; Fairchild, A. J.; Koymen, A. R.; Weiss, A. H.

2017-01-01

An advanced variable energy positron beam (~2 eV to 20 keV) has been designed, tested and utilized for coincidence Doppler broadening (CDB) measurements at the University of Texas at Arlington (UTA). A high efficiency solidified rare gas (Neon) moderator was used for the generation of a slow positron beam. The gamma rays produced as a result of the annihilation of positrons with the sample electrons are measured using a high purity Germanium (HPGe) detector in coincidence with a NaI(Tl) detector. Modifications to the system, currently underway, permits simultaneous measurements utilizing Positron annihilation induced Auger Electron Spectroscopy (PAES) and CDB. The tendency of positrons to become trapped in an image potential well at the surface will allow the new system to be used in measurements of the chemical structure of surfaces, internal or external and interfaces. The system will utilize a time of flight (TOF) technique for electron energy measurements. A 3m flight path from the sample to a micro-channel plate (MCP) in the new system will give it superior energy resolution at higher electron energies as compared to previous TOF systems utilizing shorter flight paths.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code.

NASA Astrophysics Data System (ADS)

Chacon, L.; Knoll, D. A.

2004-11-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended primitive-variable MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field, non-dissipative, and stable in the absence of physical dissipation.(L. Chacón , phComput. Phys. Comm.) submitted (2004) PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, first and second-order implicit schemes are available, although higher-order temporal implicit schemes can be effortlessly implemented within the Newton-Krylov framework. A successful, scalable, MG physics-based preconditioning strategy, similar in concept to previous 2D MHD efforts,(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002); phJ. Comput. Phys., 188 (2), 573-592 (2003) has been developed. We are currently in the process of parallelizing the code using the PETSc library, and a Newton-Krylov-Schwarz approach for the parallel treatment of the preconditioner. In this poster, we will report on both the serial and parallel performance of PIXIE3D, focusing primarily on scalability and CPU speedup vs. an explicit approach.

A 3D network of helicates fully assembled by pi-stacking interactions.

PubMed

Vázquez, Miguel; Taglietti, Angelo; Gatteschi, Dante; Sorace, Lorenzo; Sangregorio, Claudio; González, Ana M; Maneiro, Marcelino; Pedrido, Rosa M; Bermejo, Manuel R

2003-08-07

The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.

Cellular effects of bacterial N-3-Oxo-dodecanoyl-L-Homoserine lactone on the sponge Suberites domuncula (Olivi, 1792): insights into an intimate inter-kingdom dialogue.

PubMed

Gardères, Johan; Henry, Joël; Bernay, Benoit; Ritter, Andrès; Zatylny-Gaudin, Céline; Wiens, Matthias; Müller, Werner E G; Le Pennec, Gaël

2014-01-01

Sponges and bacteria have lived together in complex consortia for 700 million years. As filter feeders, sponges prey on bacteria. Nevertheless, some bacteria are associated with sponges in symbiotic relationships. To enable this association, sponges and bacteria are likely to have developed molecular communication systems. These may include molecules such as N-acyl-L-homoserine lactones, produced by Gram-negative bacteria also within sponges. In this study, we examined the role of N-3-oxododecanoyl-L-homoserine lactone (3-oxo-C12-HSL) on the expression of immune and apoptotic genes of the host sponge Suberites domuncula. This molecule seemed to inhibit the sponge innate immune system through a decrease of the expression of genes coding for proteins sensing the bacterial membrane: a Toll-Like Receptor and a Toll-like Receptor Associated Factor 6 and for an anti-bacterial perforin-like molecule. The expression of the pro-apoptotic caspase-like 3/7 gene decreased as well, whereas the level of mRNA of anti-apoptotic genes Bcl-2 Homolog Proteins did not change. Then, we demonstrated the differential expression of proteins in presence of this 3-oxo-C12-HSL using 3D sponge cell cultures. Proteins involved in the first steps of the endocytosis process were highlighted using the 2D electrophoresis protein separation and the MALDI-TOF/TOF protein characterization: α and β subunits of the lysosomal ATPase, a cognin, cofilins-related proteins and cytoskeleton proteins actin, α tubulin and α actinin. The genetic expression of some of these proteins was subsequently followed. We propose that the 3-oxo-C12-HSL may participate in the tolerance of the sponge apoptotic and immune systems towards the presence of bacteria. Besides, the sponge may sense the 3-oxo-C12-HSL as a molecular evidence of the bacterial presence and/or density in order to regulate the populations of symbiotic bacteria in the sponge. This study is the first report of a bacterial secreted molecule acting on sponge cells and regulating the symbiotic relationship.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

PubMed

Bizzini, A; Greub, G

2010-11-01

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Externally initiated regioregular P3HT with controlled molecular weight and narrow polydispersity.

PubMed

Bronstein, Hugo A; Luscombe, Christine K

2009-09-16

The ability of chemists to design and synthesize pi-conjugated organic polymers with precise control remains the key to technological breakthroughs for using polymer materials in electronic and photonic devices. In this communication, the controlled chain-growth polymerization of regioregular poly(3-hexylthiophene) (P3HT) from an external initiator using 1,3-bis(diphenylphosphino)propane (dppp) as a catalyst ligand is reported. The complexes cis-chloro(phenyl)(dppp)nickel(II) and cis-chloro(o-tolyl)(dppp)nickel(II) were synthesized and characterized by (31)P NMR spectroscopy. These complexes served as initiators in the polymerization of 2-bromo-5-chloromagnesio-3-hexylthiophene in THF at room temperature, affording fully regioregular P3HT with controlled molecular weights and narrow molecular weight distributions, as demonstrated by gel-permeation chromatography and (1)H NMR spectroscopy. MALDI-TOF mass spectrometry revealed that the polymers had almost complete incorporation of the initiating aryl group, and when the aryl group was o-tolyl, only Tol/H end groups were observed. Although external initiators have been used previously with a PPh(3) ligand, that methodology led to polymers with broad molecular weight distributions. This is the first example in which complete control over the externally initiated P3HT polymerization has been achieved.

MALDI-TOF mass spectrometry for early identification of bacteria grown in blood culture bottles.

PubMed

Zabbe, Jean-Benoît; Zanardo, Laura; Mégraud, Francis; Bessède, Emilie

2015-08-01

This note reports an interesting way to rapidly identify bacteria grown from blood culture bottles. Chocolate agar plates were inoculated with 1 drop of the positive blood bottle medium. After a 3-hour incubation, the growth veil was submitted to MALDI-TOF mass spectrometry: 77% of the bacteria present have been correctly identified. Copyright © 2015 Elsevier B.V. All rights reserved.

Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam.

PubMed

Doan, N T L; Van Hoorde, K; Cnockaert, M; De Brandt, E; Aerts, M; Le Thanh, B; Vandamme, P

2012-10-01

To evaluate the potential use of MALDI-TOF MS for fast and reliable classification and identification of lactic acid bacteria (LAB) from traditional fermented foods. A total of 119 strains of LAB from fermented meat (nem chua) were analysed with both (GTG)(5)-PCR fingerprinting and MALDI-TOF MS. Cluster analysis of the profiles revealed five species represented by a single isolate both in (GTG)(5)-PCR and in MALDI-TOF MS; five species grouped alike for (GTG)(5)-PCR and for MALDI-TOF MS; however, differences in minimal similarity between the delineated (GTG)(5)-PCR and MALDI-TOF MS clusters could be observed; three species showed more heterogeneity in their MALDI-TOF MS profiles compared to their (GTG)(5)-PCR profiles; two species, each represented by a single MALDI-TOF cluster, were subdivided in the corresponding (GTG)(5)-PCR dendrogram. As proof of the identification potential of MALDI-TOF MS, LAB diversity from one fermented mustard sample was analysed using MALDI-TOF MS. PheS gene sequencing was used for validation. MALDI-TOF MS is a powerful, fast, reliable and cost-effective technique for the identification of LAB associated with the production of fermented foods. Food LAB can be identified using MALDI-TOF MS, and its application could possibly be extended to other food matrices and/or other food-derived micro-organisms. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium. Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result. Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our approach allowed an optimized treatment recommendation. MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation. Copyright © 2015 Elsevier GmbH. All rights reserved.

Fully 3D modeling of tokamak vertical displacement events with realistic parameters

NASA Astrophysics Data System (ADS)

Pfefferle, David; Ferraro, Nathaniel; Jardin, Stephen; Bhattacharjee, Amitava

2016-10-01

In this work, we model the complex multi-domain and highly non-linear physics of Vertical Displacement Events (VDEs), one of the most damaging off-normal events in tokamaks, with the implicit 3D extended MHD code M3D-C1. The code has recently acquired the capability to include finite thickness conducting structures within the computational domain. By exploiting the possibility of running a linear 3D calculation on top of a non-linear 2D simulation, we monitor the non-axisymmetric stability and assess the eigen-structure of kink modes as the simulation proceeds. Once a stability boundary is crossed, a fully 3D non-linear calculation is launched for the remainder of the simulation, starting from an earlier time of the 2D run. This procedure, along with adaptive zoning, greatly increases the efficiency of the calculation, and allows to perform VDE simulations with realistic parameters and high resolution. Simulations are being validated with NSTX data where both axisymmetric (toroidally averaged) and non-axisymmetric induced and conductive (halo) currents have been measured. This work is supported by US DOE Grant DE-AC02-09CH11466.

Electropolymerizable peripherally tetra-{2-[3-(diethylamino)phenoxy]ethoxy} substituted as well as axially (4-phenylpiperazin-1-yl)propanoxy-disubstituted silicon phthalocyanines and their electrochemistry.

PubMed

Biyiklioglu, Zekeriya; Alp, Hakan

2015-11-21

A novel type of peripherally tetra-substituted as well as axially disubstituted silicon(iv) phthalocyanine containing electropolymerizable ligands was designed and synthesized for the first time. Axial bis-hydroxy silicon phthalocyanine 2 was prepared from 2(3),9(10),16(17),23(24)-tetrakis-{2-[3-(diethylamino)phenoxy]ethoxy}phthalocyanine 1 in dichloromethane by using 1.8-diazabicyclo[5.4.0]undec-7-ene (DBU) and trichlorosilane. Peripherally tetra and axially di-substituted silicon phthalocyanine 4 was synthesized from 2(3),9(10),16(17),23(24)-tetrakis-{2-[3-(diethylamino)phenoxy]ethoxy}silicon(iv)phthalocyanine dihydroxide 2 with 1-(3-chloropropyl)-4-phenylpiperazine 3 in toluene in the presence of NaH at 120 °C. These complexes were fully characterized by various spectroscopy techniques such as (1)H-NMR, (13)C-NMR, IR, UV-Vis, and MALDI-TOF spectroscopy and elemental analysis as well. Electropolymerization properties of silicon(IV) phthalocyanine complexes were investigated by cyclic and square wave voltammetry. Electrochemical studies reveal that silicon(IV) phthalocyanine complexes were electropolymerized on the working electrode during the anodic potential scan. This study is the first example of electropolymerization of both peripherally tetra and axially di-substituted silicon phthalocyanines on the same molecule.

Topochemical Analysis of Cell Wall Components by TOF-SIMS.

PubMed

Aoki, Dan; Fukushima, Kazuhiko

2017-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a recently developing analytical tool and a type of imaging mass spectrometry. TOF-SIMS provides mass spectral information with a lateral resolution on the order of submicrons, with widespread applicability. Sometimes, it is described as a surface analysis method without the requirement for sample pretreatment; however, several points need to be taken into account for the complete utilization of the capabilities of TOF-SIMS. In this chapter, we introduce methods for TOF-SIMS sample treatments, as well as basic knowledge of wood samples TOF-SIMS spectral and image data analysis.

Differentially expressed proteins among normal cervix, cervical intraepithelial neoplasia and cervical squamous cell carcinoma.

PubMed

Zhao, Q; He, Y; Wang, X-L; Zhang, Y-X; Wu, Y-M

2015-08-01

To explore the differentially expressed proteins in normal cervix, cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (CSCC) tissues by differential proteomics technique. Cervical tissues (including normal cervix, CIN and CSCC) were collected in Department of Gynecologic Oncology of Beijing Obstetrics and Gynecology Hospital. Two-dimensional fluorescence difference in gel electrophoresis (2-D DIGE) and DeCyder software were used to detect the differentially expressed proteins. Matrix-assisted laser desorption/ionization-time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) was used to identify the differentially expressed proteins. Western blot (WB) and immunohistochemistry (IHC) were performed to validate the expressions of selected proteins among normal cervix, CIN and CSCC. 2-D DIGE images with high resolution and good repeatability were obtained. Forty-six differentially expressed proteins (27 up-regulated and 19 down-regulated) were differentially expressed among the normal cervix, CIN and CSCC. 26 proteins were successfully identified by MALDI-TOF/TOF MS. S100A9 (S100 calcium-binding protein A9) was the most significantly up-regulated protein. Eukaryotic elongation factor 1-alpha-1 (eEF1A1) was the most significantly down-regulated protein. Pyruvate kinase isozymes M2 (PKM2) was both up-regulated and down-regulated. The results of WB showed that with the increase in the severity of cervical lesions, the expression of S100A9 protein was significantly increased among the three groups (P = 0.010). The expression of eEF1A1 was reduced but without significant difference (P = 0.861). The expression of PKM2 was significantly reduced (P = 0.000). IHC showed that protein S100A9 was mainly expressed in the cytoplasm, and its positive expression rate was 20.0 % in normal cervix, 70.0 % in CIN and 100.0 % in CSCC, with a significant difference among them (P = 0.006). eEF1A1 was mainly expressed in the cell plasma, and its positive expression rate was 70.0 % in normal cervix, 73.3 % in CIN and 60.0 % in CSCC tissues, without significant difference among them (P = 0.758). PKM2 was mainly expressed in the cell nuclei, and its positive expression rate was 100.0 % in normal cervix, 93.3 % in CIN and 75.0 % in CSCC tissues, showing a difference close to statistical significance (P = 0.059) among them. There are differentially expressed proteins among normal cervix, CIN and CSCC. S100A9, eEF1A1 and PKM2 may become candidate markers for early diagnosis of cervical cancer and new targets for therapy. It also provides a basis for further studies of the mechanism for CIN developing to CSCC.

An universal read-out controller

NASA Astrophysics Data System (ADS)

Manz, S.; Abel, N.; Gebelein, J.; Kebschull, U.

2010-11-01

Since 2007 we design and develop a ROC (read-out controller) for FAIR's data-acquisition. While our first implementation solely focused on the nXYTER, today we are also designing and implementing readout logic for the GET4 which is supposed to be part of the ToF detector. Furthermore, we fully support both Ethernet and Optical transport as two transparent solutions. The usage of a strict modularization of the Read Out Controller enables us to provide an Universal ROC where front-end specific logic and transport logic can be combined in a very flexible way. Fault tolerance techniques are only required for some of those modules and hence are only implemented there.

PET optimization for improved assessment and accurate quantification of {sup 90}Y-microsphere biodistribution after radioembolization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martí-Climent, Josep M., E-mail: jmmartic@unav.es; Prieto, Elena; Elosúa, César

2014-09-15

Purpose: {sup 90}Y-microspheres are widely used for the radioembolization of metastatic liver cancer or hepatocellular carcinoma and there is a growing interest for imaging {sup 90}Y-microspheres with PET. The aim of this study is to evaluate the performance of a current generation PET/CT scanner for {sup 90}Y imaging and to optimize the PET protocol to improve the assessment and the quantification of {sup 90}Y-microsphere biodistribution after radioembolization. Methods: Data were acquired on a Biograph mCT-TrueV scanner with time of flight (TOF) and point spread function (PSF) modeling. Spatial resolution was measured with a{sup 90}Y point source. Sensitivity was evaluated usingmore » the NEMA 70 cm line source filled with {sup 90}Y. To evaluate the count rate performance, {sup 90}Y vials with activity ranging from 3.64 to 0.035 GBq were measured in the center of the field of view (CFOV). The energy spectrum was evaluated. Image quality with different reconstructions was studied using the Jaszczak phantom containing six hollow spheres (diameters: 31.3, 28.1, 21.8, 16.1, 13.3, and 10.5 mm), filled with a 207 kBq/ml {sup 90}Y concentration and a 5:1 sphere-to-background ratio. Acquisition time was adjusted to simulate the quality of a realistic clinical PET acquisition of a patient treated with SIR-Spheres{sup ®}. The developed methodology was applied to ten patients after SIR-Spheres{sup ®} treatment acquiring a 10 min per bed PET. Results: The energy spectrum showed the{sup 90}Y bremsstrahlung radiation. The {sup 90}Y transverse resolution, with filtered backprojection reconstruction, was 4.5 mm in the CFOV and degraded to 5.0 mm at 10 cm off-axis. {sup 90}Y absolute sensitivity was 0.40 kcps/MBq in the center of the field of view. Tendency of true and random rates as a function of the {sup 90}Y activity could be accurately described using linear and quadratic models, respectively. Phantom studies demonstrated that, due to low count statistics in {sup 90}Y PET acquisition, the optimal parameters for the standard OSEM+PSF reconstruction were only one iteration and a postreconstruction filter of 6 mm FWHM, for both TOF and non-TOF reconstructions. Moreover, when TOF is included, the signal to noise ratio increased and visibility achieved 100% by the experienced observers and 93.3% according to the Rose model of statistical detection. In 50% of patients, TOF allowed the visualization of {sup 90}Y radioembolized lesions not seen without TOF, confirming phantom results. Liver activity was accurately quantified, with no significant differences between reconstructed and actual delivered activity to the whole-liver [mean relative difference (10.2 ± 14.7)%]. Conclusions: Qualitative and quantitative{sup 90}Y PET imaging improved with the introduction of TOF in a PET/CT scanner, thereby allowing the visualization of microsphere deposition in lesions not visible in non-TOF images. This technique accurately quantifies the total activity delivered to the liver during radioembolization with {sup 90}Y-microspheres and allows dose estimation.« less

Rapid Genotyping of Single Nucleotide Polymorphisms Influencing Warfarin Drug Response by Surface-Enhanced Laser Desorption and Ionization Time-of-Flight (SELDI-TOF) Mass Spectrometry

PubMed Central

Yang, Shangbin; Xu, LiHui; Wu, Haifeng M.

2010-01-01

Warfarin exhibits significant interindividual variability in dosing requirements. Different drug responses are partly attributed to the single nucleotide polymorphisms (SNPs) that influence either drug action or drug metabolism. Rapid genotyping of these SNPs helps clinicians to choose appropriate initial doses to quickly achieve anticoagulation effects and to prevent complications. We report a novel application of surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) in the rapid genotyping of SNPs that impact warfarin efficacy. The SNPs were first amplified by PCR and then underwent single base extension to generate the specific SNP product. Next, genetic variants displaying different masses were bound to Q10 anionic proteinChips and then genotyped by using SELDI-TOF MS in a multiplex fashion. SELDI-TOF MS offered unique properties of on-chip sample enrichment and clean-ups, which streamlined the testing procedures and eliminated many tedious experimental steps required by the conventional MS-based method. The turn-around time for genotyping three known warfarin-related SNPs, CYP2C9*2, CYP2C9*3, and VKORC1 3673G>A by SELDI-TOF MS was less than 5 hours. The analytical accuracy of this method was confirmed both by bidirectional DNA sequencing and by comparing the genotype results (n = 189) obtained by SELDI-TOF MS to reports from a clinical reference laboratory. This new multiplex genotyping method provides an excellent clinical laboratory platform to promote personalized medicine in warfarin therapy. PMID:20075209

Rapid genotyping of single nucleotide polymorphisms influencing warfarin drug response by surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) mass spectrometry.

PubMed

Yang, Shangbin; Xu, LiHui; Wu, Haifeng M

2010-03-01

Warfarin exhibits significant interindividual variability in dosing requirements. Different drug responses are partly attributed to the single nucleotide polymorphisms (SNPs) that influence either drug action or drug metabolism. Rapid genotyping of these SNPs helps clinicians to choose appropriate initial doses to quickly achieve anticoagulation effects and to prevent complications. We report a novel application of surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) in the rapid genotyping of SNPs that impact warfarin efficacy. The SNPs were first amplified by PCR and then underwent single base extension to generate the specific SNP product. Next, genetic variants displaying different masses were bound to Q10 anionic proteinChips and then genotyped by using SELDI-TOF MS in a multiplex fashion. SELDI-TOF MS offered unique properties of on-chip sample enrichment and clean-ups, which streamlined the testing procedures and eliminated many tedious experimental steps required by the conventional MS-based method. The turn-around time for genotyping three known warfarin-related SNPs, CYP2C9*2, CYP2C9*3, and VKORC1 3673G>A by SELDI-TOF MS was less than 5 hours. The analytical accuracy of this method was confirmed both by bidirectional DNA sequencing and by comparing the genotype results (n = 189) obtained by SELDI-TOF MS to reports from a clinical reference laboratory. This new multiplex genotyping method provides an excellent clinical laboratory platform to promote personalized medicine in warfarin therapy.

Radiative neutron capture on 242Pu in the resonance region at the CERN n_TOF-EAR1 facility

NASA Astrophysics Data System (ADS)

Lerendegui-Marco, J.; Guerrero, C.; Mendoza, E.; Quesada, J. M.; Eberhardt, K.; Junghans, A. R.; Krtička, M.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Bacak, M.; Balibrea, J.; Barbagallo, M.; Barros, S.; Bečvář, F.; Beinrucker, C.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Cosentino, L.; Damone, L. A.; Diakaki, M.; Dietz, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Furman, V.; Göbel, K.; García, A. R.; Gawlik, A.; Glodariu, T.; Gonçalves, I. F.; González-Romero, E.; Goverdovski, A.; Griesmayer, E.; Gunsing, F.; Harada, H.; Heftrich, T.; Heinitz, S.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lo Meo, S.; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Musumarra, A.; Nolte, R.; Oprea, A.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, J. I.; Praena, J.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Rout, P. C.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Stamatopoulos, A.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Weiss, C.; Wolf, C.; Woods, P. J.; Wright, T.; Žugec, P.; n TOF Collaboration

2018-02-01

The spent fuel of current nuclear reactors contains fissile plutonium isotopes that can be combined with uranium to make mixed oxide (MOX) fuel. In this way the Pu from spent fuel is used in a new reactor cycle, contributing to the long-term sustainability of nuclear energy. However, an extensive use of MOX fuels, in particular in fast reactors, requires more accurate capture and fission cross sections for some Pu isotopes. In the case of 242Pu there are sizable discrepancies among the existing capture cross-section measurements included in the evaluations (all from the 1970s) resulting in an uncertainty as high as 35% in the fast energy region. Moreover, postirradiation experiments evaluated with JEFF-3.1 indicate an overestimation of 14% in the capture cross section in the fast neutron energy region. In this context, the Nuclear Energy Agency (NEA) requested an accuracy of 8% in this cross section in the energy region between 500 meV and 500 keV. This paper presents a new time-of-flight capture measurement on 242Pu carried out at n_TOF-EAR1 (CERN), focusing on the analysis and statistical properties of the resonance region, below 4 keV. The 242Pu(n ,γ ) reaction on a sample containing 95(4) mg enriched to 99.959% was measured with an array of four C6D6 detectors and applying the total energy detection technique. The high neutron energy resolution of n_TOF-EAR1 and the good statistics accumulated have allowed us to extend the resonance analysis up to 4 keV, obtaining new individual and average resonance parameters from a capture cross section featuring a systematic uncertainty of 5%, fulfilling the request of the NEA.

The potential role of IDEAL MRI for identification of lipids and hemorrhage in carotid artery plaques.

PubMed

Khosa, Faisal; Clough, Rachel E; Wang, Xiaoen; Madhuranthakam, Ananth J; Greenman, Robert L

2018-06-01

Hemorrhage and lipid deposits contribute to instability in atherosclerotic plaques. Unstable carotid artery plaques can lead to cerebral ischemic events. While MRI studies have shown the ability to identify plaque components, the identification of hemorrhage and lipids has proven to be problematic. The purpose of this study was to quantitatively evaluate the potential of the MRI fat/water separation method known as iterative decomposition of water and fat with echo asymmetry and least squares estimation (IDEAL) to complement and improve existing methods for the identification of hemorrhage and lipids in carotid artery plaques. Fifteen asymptomatic subjects with 50-79% stenosis of at least one carotid artery were enrolled. Hemorrhage and lipid components within carotid plaques were identified using previously published criteria based on the multiple contrast-weighted (MCW) method (3D Time-of-Flight (3D-TOF), T1-Weighted (T1W) and T2-Weighted (T2W)). The hemorrhage:muscle, lipid:muscle and intra-plaque lipid:hemorrhage signal intensity ratios (SIR) and contrast to noise ratios (CNR) were measured on MCW and compared to IDEAL black-blood images. No differences were found between any of the MCW methods for any of the SIRs measured. The IDEAL Fat images had higher lipid:muscle and lipid/hemorrhage SIRs (p<0.001) compared to IDEAL Water and all MCW image sequence types. The mean values of IDEAL Fat hemorrhage:muscle SIR and CNR were nearly unity (1.1±0.6) and nearly zero (0.1±1.1), respectively. The IDEAL Water imaging was not significantly different than any of the MCW methods for any of the SIRs or for the hemorrhage:muscle CNR of 3D-TOF, while its CNRs were significantly higher than IDEAL Fat lipid:muscle (p<0.05) and lipid:hemorrhage (p<0.001) and all MCW methods (p<0.001). The addition of IDEAL Water and Fat imaging to the MCW method shows potential to improve the identification of hemorrhage and lipid structures in carotid artery plaques. Copyright © 2017 Elsevier Inc. All rights reserved.

A SPAD-based 3D imager with in-pixel TDC for 145ps-accuracy ToF measurement

NASA Astrophysics Data System (ADS)

Vornicu, I.; Carmona-Galán, R.; Rodríguez-Vázquez, Á.

2015-03-01

The design and measurements of a CMOS 64 × 64 Single-Photon Avalanche-Diode (SPAD) array with in-pixel Time-to-Digital Converter (TDC) are presented. This paper thoroughly describes the imager at architectural and circuit level with particular emphasis on the characterization of the SPAD-detector ensemble. It is aimed to 2D imaging and 3D image reconstruction in low light environments. It has been fabricated in a standard 0.18μm CMOS process, i. e. without high voltage or low noise features. In these circumstances, we are facing a high number of dark counts and low photon detection efficiency. Several techniques have been applied to ensure proper functionality, namely: i) time-gated SPAD front-end with fast active-quenching/recharge circuit featuring tunable dead-time, ii) reverse start-stop scheme, iii) programmable time resolution of the TDC based on a novel pseudo-differential voltage controlled ring oscillator with fast start-up, iv) a global calibration scheme against temperature and process variation. Measurements results of individual SPAD-TDC ensemble jitter, array uniformity and time resolution programmability are also provided.

Sensitivity enhancement of fluorescence detection in CE by coupling and conducting excitation light with tapered optical fiber.

PubMed

Yang, Xiupei; Huo, Feng; Yuan, Hongyan; Zhang, Bo; Xiao, Dan; Choi, Martin M F

2011-01-01

This paper reports the enhancement of sensitivity of detection for in-column fiber optic-induced fluorescence detection system in CE by tapered optical fiber (TOF). Two types of optical fiber, TOF and conventional cylindrical optical fiber (COF), were employed to construct the CE (TOF-CE and COF-CE) and were compared for sensitivity to riboflavin (RF). The fluorescence intensities from a RF sample with excitation light sources and fibers at various coupling angles were investigated. The fluorescence signal from TOF-CE was ca. ten times that of COF-CE. In addition, the detection performance of four excitation light source-fiber configurations including Laser-TOF, Laser-COF, LED-TOF, and LED-COF were compared. The LODs for RF were 0.21, 0.82, 0.80, and 7.5 nM, respectively, for the four excitation light source-fiber configurations. The results demonstrate that the sensitivity obtained by LED-TOF is close to that of Laser-COF. Both Laser-TOF and LED-TOF can greatly improve the sensitivity of detection in CE. TOF has the major attribute of collecting and focusing the excitation light intensity. Thus, the sensitivity obtained by LED-TOF without focusing lens is just same as that of LED-COF with a focusing lens. This demonstrates that the CE system can be further simplified by eliminating the focusing lens for excitation light. LED-TOF-CE and LED-COF-CE system were applied to the separation and determination of RF in real sample (green tea), respectively. The tapered fiber optic-induced fluorescence detection system in CE is an ideal tool for trace analysis. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sugammadex given for rocuronium-induced neuromuscular blockade in infants: a retrospectıve study.

PubMed

Ozmete, Ozlem; Bali, Cagla; Cok, Oya Yalcin; Turk, Hatice Evren Eker; Ozyilkan, Nesrın Bozdogan; Civi, Soner; Aribogan, Anıs

2016-12-01

To evaluate the efficacy and safety of sugammadex in reversing profound neuromuscular block induced by rocuronium in infant patients. Retrospective observational study. University teaching hospital. Twenty-six infants (2-12 months of age; 3-11 kg) with an American Society of Anesthesiologists classification I, II, or III who were scheduled to undergo neurosurgical procedures were included in the study. Anesthesia was induced with 5 mg/kg thiopental, 1 μg/kg fentanyl and 0.6 mg/kg rocuronium. Sevoflurane was administered to all patients after intubation. The neuromuscular block was monitored with acceleromyography using train-of-four (TOF) stimuli. Patients received additional doses of rocuronium to maintain a deep block during surgery. If profound neuromuscular block (TOF, 0) persisted at the end of the surgery, 3mg/kg sugammadex was administered. The demographic data, surgeries, and anesthetic agents were recorded. The time from sugammadex administration to recovery of neuromuscular function (TOF ratio, >0.9) and complications during and after extubation were also recorded. Twenty-six infants who had a deep neuromuscular block (TOF, 0) at the end of surgery received 3 mg/kg sugammadex. The mean recovery time of the T4/T1 ratio of 0.9 was 112 seconds. No clinical evidence of recurarization or residual curarization was observed. The efficacy and safety of sugammadex were confirmed in infant surgical patients for reversal of deep neuromuscular block induced by rocuronium. Copyright © 2016 Elsevier Inc. All rights reserved.