Resolution Window Research Articles

Application of quadrupole-Orbitrap high-resolution mass spectrometry in rapid screening and identification of synthetic dyes in herbal medicines

In this work, a method combining ultra-high performance liquid chromatography and hybrid quadrupole-Orbitrap high-resolution mass spectrometry (HR-MS) was developed and validated for use in the simultaneous screening, identification, and quantification of 21 synthetic dyes in herbal medicines. To optimize the chromatographic conditions, we used a combined Full mass scan and data-dependent MS/MS (Full MS/dd-MS2) approach in positive and negative ion mode. Under this mode, selected ions with given fragmentation energy were subjected to a dd-MS2 scan following a Full MS scan. The selectivity of this method was effectively improved using 70,000 full width at half maximum mass resolution and narrow mass window (typically 5 ppm), and a single injection was sufficient for simultaneous identification and quantification of 21 synthetic dyes within 10 min. The combined method was fully validated and complies with all criteria for selectivity, sensitivity, calibration curve linearity, accuracy, precision, recovery, matrix effect, and stability. All analytes showed excellent linear relationships as all the coefficients of determination (r2) are greater than 0.9978 over wide ranges of concentrations (e.g. 1.0-500 ng/mL for sunset yellow). The validated method was employed to detect synthetic dyes in herbal medicines and was demonstrated to provide a reliable technical basis for drug regulation and public health protection.

A new age model for the Ordovician (Sandbian) K-bentonites in Oslo, Norway

During the Late Ordovician, large explosive volcanic eruptions deposited worldwide K-bentonites, including the Millbrig and Deicke K-bentonites in North America and the Kinnekulle K-bentonite in Scandinavia. We have studied a classical locality in Oslo containing one of the most complete sections of K-bentonites in Europe.In a 53 m section of Sandbian age, we discovered 33 individual K-bentonite beds, the most notable beds being the Kinnekulle and the upper Grimstorp K-bentonite. Magnetic susceptibility (MS) measurements on two intervals show significant periodicity peaks interpreted as Milankovitch cycles and thus astronomically forced changes in sediment supply and composition. These cycles fit remarkably well with both the expected Milankovitch periodicities for the Ordovician as well as the radiometric ages presented in this study and may represent one of the most convincing demonstrations of Milankovitch cycles from the lower Paleozoic so far. Five of the K-bentonites have been dated by high-precision chemical abrasion-thermal ionization mass spectrometry (CA-TIMS) U-Pb zircon geochronology, where the Kinnekulle K-bentonite gives an age of 454.06 ± 0.43 Ma. We have integrated the new data and calculated an age model showing the sedimentation rates through the section and thereby the ages of each of the 33 K-bentonites. Using the age model, we further present a new age for the Sandbian-Katian stage boundary. The section in Oslo provides the highest resolution window into the Upper Ordovician K-bentonite succession so far and helps shed more light on the chronology of one of the most intense volcanic periods of the Paleozoic and the relationship with the global carbon cycle changes that followed.

An EDUGATE simulation toolkit based on the educational easyPET

EasyPET is a new concept of a Positron Emission Tomography (PET) scanner using an innovative acquisition method based on two rotation axes for the movement of detector pairs. Due to its simplicity, it is suitable for education purposes, to teach students about the PET technology and its basic concepts, from the radiation detecting and analogue pulse analysis to the coincidence sorting and image reconstruction. The concept allows achieving high and uniform position resolution over the whole field of view (FoV), by eliminating parallax errors due to the depth of interaction (DoI), which are typical of ring-based PET systems, so quality images are obtained even without state-of-the-art image reconstruction algorithms. The technology developed at the University of Aveiro with a patent-pending, is licensed to CAEN S.p.A, and included in the educational catalogue of the company. In this work, a simulation toolkit based in the Edugate platform was developed to simulate the EasyPET system. It can simulate all the physical aspects of the product, such us the scanning range, variable Field-of-View (FOV), scintillator energy resolution, coincidence time and energy window, among others. A simple image reconstruction algorithm based on Filtered-back-projection (FBP) is implemented. The toolkit allows a quick analysis in classroom of the simulation results. The platform was also used to study the new EasyPET 3D version, and a simulation of a NEMA NU 4-2008 IQ phantom was performed, demonstrating the capability of the platform not only for education purposes but also for research. Patent Universidade de Aveiro: PCT/IB2016/051487.

ProgressER

Entity resolution (ER) is the process of identifying which entities in a dataset refer to the same real-world object. In relational ER, the dataset consists of multiple entity-sets and relationships among them. Such relationships cause the resolution of some entities to influence the resolution of other entities. For instance, consider a relational dataset that consists of a set of research paper entities and a set of venue entities. In such a dataset, deciding that two research papers are the same may trigger the fact that their venues are also the same. This article proposes a progressive approach to relational ER, named ProgressER, that aims to produce the highest quality result given a constraint on the resolution budget, specified by the user. Such a progressive approach is useful for many emerging analytical applications that require low latency response (and thus cannot tolerate delays caused by cleaning the entire dataset) and/or in situations where the underlying resources are constrained or costly to use. To maximize the quality of the result, ProgressER follows an adaptive strategy that periodically monitors and reassesses the resolution progress to determine which parts of the dataset should be resolved next and how they should be resolved. More specifically, ProgressER divides the input budget into several resolution windows and analyzes the resolution progress at the beginning of each window to generate a resolution plan for the current window. A resolution plan specifies which blocks of entities and which entity pairs within blocks need to be resolved during the plan execution phase of that window. In addition, ProgressER specifies, for each identified pair of entities, the order in which the similarity functions should be applied on the pair. Such an order plays a significant role in reducing the overall cost because applying the first few functions in this order might be sufficient to resolve the pair. The empirical evaluation of ProgressER demonstrates its significant advantage in terms of progressiveness over the traditional ER techniques for the given problem settings.

Physical basis of the \u2018magnification rule\u2019 for standardized Immunohistochemical scoring of HER2 in breast and gastric cancer

BackgroundDetection of HER2/neu receptor overexpression and/or amplification is a prerequisite for efficient anti-HER2 treatment of breast and gastric carcinomas. Immunohistochemistry (IHC) of the HER2 protein is the most common screening test, thus precise and reproducible IHC-scoring is of utmost importance. Interobserver variance still is a problem; in particular in gastric carcinomas the reliable differentiation of IHC scores 2+ and 1+ is challenging.Herein we describe the physical basis of what we called the ‘magnification rule’: Different microscope objectives are employed to reproducibly subdivide the continuous spectrum of IHC staining intensities into distinct categories (1+, 2+, 3+).MethodsHER2-IHC was performed on 120 breast cancer biopsy specimens (n = 40 per category). Width and color-intensity of membranous DAB chromogen precipitates were measured by whole-slide scanning and digital morphometry. Image-analysis data were related to semi-quantitative manual scoring according to the magnification rule and to the optical properties of the employed microscope objectives.ResultsThe semi-quantitative manual HER2-IHC scores are correlated to color-intensity measured by image-analysis and to the width of DAB-precipitates. The mean widths ±standard deviations of precipitates were: IHC-score 1+, 0.64 ± 0.1 μm; score 2+, 1.0 ± 0.23 μm; score 3+, 2.14 ± 0.4 μm. The width of precipitates per category matched the optical resolution of the employed microscope objective lenses: Approximately 0.4 μm (40×), 1.0 μm (10×) and 2.0 μm (5×).ConclusionsPerceived intensity, width of the DAB chromogen precipitate, and absolute color-intensity determined by image-analysis are linked. These interrelations form the physical basis of the ‘magnification rule’: 2+ precipitates are too narrow to be observed with 5× microscope objectives, 1+ precipitates are too narrow for 10× objectives. Thus, the rule uses the optical resolution windows of standard diagnostic microscope objectives to derive the width of the DAB-precipitates. The width is in turn correlated with color-intensity. Hereby, the more or less subjective estimation of IHC scores based only on the staining-intensity is replaced by a quasi-morphometric measurement. The principle seems universally applicable to immunohistochemical stainings of membrane-bound biomarkers that require an intensity-dependent scoring.

Congenital Extra-Cardiac Vascular Anomalies as Detected on Multislice Computed Tomography Angiography

Background: Accurate evaluation of extra cardiac and intra cardiac anomalies in congenital heart diseases (CHD) is vital for diagnosis and treatment. Trans-thoracic echocardiography (TTE) is the classical choice for children suspected to have CHD because TTE is safe, readily available and its capacity to perform Doppler flow studies therefore can measure hemodynamic parameters. Plus its ability to evaluate intra cardiac abnormalities like atrial septal defect and ventricular septal defect. Therefore, owing to its lower spatial resolution and limited acoustic window; it is not precise in evaluation of extra cardiac abnormalities. Aim of the Work: to evaluate the advantage of recent advances of ECG gated MDCT in diagnosis of congenital heart disease in pediatrics and assessment of associated extra cardiac abnormalities within the great vessels in comparison with echocardiography findings. Patients and Methods: The current study was carried out on 36 patients in Radio-diagnosis Department, Faculty of medicine, Ain Shams University and specialized private radiology centers. The patients were referred from pediatric hospital, cardiology clinic with their echocardiographic reports to radio-diagnosis department, cardiac imaging unit with a view to execute ECG- gated multi-slice CT of the heart & extra-cardiac great vessels. Results: In this study aortic anomalies represent the most common extra-cardiac anomalies accounting for 36.5% of our cases while comprising: Supravalvular aortic stenosis; 4.3%, Aortic CoA; 26.1%, arch anomalies with vascular rings; 52.2% and finally anomalous coronary arteries; 17.4%. By Using MDCT we were able to delineate eight cases of right aortic arch (RAA).Two of them with aberrant left subclavian artery (ALSCA) adding to two cases of left aortic arch with an aberrant right subclavian artery (ARSCA). On the other hand ,TTE failed to identify 6 cases of RAA with a sensitivity 75%, specificity 100%, NPV 96.61% and one case of ALSCA with a sensitivity 50.0%, specificity 100%, NPV 98.41% .Regarding coronary anomalies , Cardiac CTA succeeded in characterization of origin and course of all coronary abnormalities encountered in our study encompassing 4 cases specifically anomalous LAD from right coronary sinus running a prepulmonic course anterior to RVOT , RCA from LAD and single coronary artery adding to LCX- RV coronary fistula. While TTE failed to depict two cases of the coronary anomalies with a sensitivity of 50%, specificity 100%, PPV 100% and NPV 96.83%. Conclusion: CTA can provide the confident detection and exclusion of extra- cardiac vascular abnormalities with superb anatomical description which was feasible with a sensitivity 98.41%, specificity 99.76%, PPV 96.88% and NPV 99.88%.

A LC-HRMS After QuEChERS Cleanup Method for the Rapid Determination of Dye Residues in Fish Products

The reliability of a rapid LC-HRMS method was studied in order to find a sensitive and accurate, simple, cheap, and rapid method for screening and quantitative determination of malachite green (MG), leucomalachite green (LMG), brilliant green (BG), crystal violet (CV), and leucocrystal violet (LCV) in fish muscle. All the analytes were extracted using a mixture of acetonitrile and citrate buffer, while the cleanup phase was carried out by Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) method. All the data analyzed were acquired using both full MS and dd-MS2 modes. Good specificity, precision (relative standard deviation <11% for each sample tested), recovery (10–60%), decision limit (CCα between 0.55 and 0.62 μg kg−1), detection capabilities (CCβ between 0.65 and 0.78 μg kg−1), and ruggedness were achieved for the reliability of the method. Satisfactory results were obtained during the linearity test in the range of 0.10–2 ng mL−1 (r 2 > 0.999). Best recoveries were obtained by the QuEChERS cleanup method for all the analytes examined, presenting values between 70 and 104%. The application of 70,000 FWHM mass resolution and narrow mass windows significantly improved the selectivity of the method, leading to simultaneous screening and quantification of dye residues in comparison to other methods proposed in literature. The optimized method proposed in this work enables a simple and fast preparation; it offers exceptional sensitivity and selectivity and maximizes efficiency and reproducibility with a low consumption of reagents. Finally, the present method was successfully employed to detect dye residues in 73 fish samples, as provided for the national residue control plan.

Continuous Wavelet Transform Based Spectral Decomposition of 3d Seismic Data for Reservoir Characterization in Oyi Field, se Niger Delta

Continuous Wavelet Transform (CWT) is one of the most used wavelet transform based spectral decomposition methods in the direct detection of hydrocarbons and as an indicator of stratigraphic variability due to its optimal time-frequency resolution and variable time window requirements. CWT based spectral decomposition was applied on a 3D Post Stack Time Migrated (PSTM) seismic data acquired over a producing field using morlet wavelet and a time varying analysis window. Frequency amplitude slices of 10 Hz to 50 Hz were extracted from a 1625 ms HD1 seismic horizon and analyzed for possible hydrocarbon indications and stratigraphy. Hydrocarbon filled reservoir sands were delineated as low frequency high amplitude spectral anomalies between 20 Hz to 30 Hz frequency band coincident with the locations of producing wells in the field. Also, high frequency high amplitude spectral anomaly were delineated at predominantly 50 Hz frequency indicating a thin-bed with probable hydrocarbon saturation particularly gas, suspected to be a bypass hydrocarbon zone. Result also shows amplitude diminution with increasing frequency attributed to local variations in lithology. Therefore, appropriate application of this method will improve reservoir characterization and enhanced bed thickness definition, de-risk prospects and minimize dry well drilling in the field.

Tipping solutions: emerging 3D nano-fabrication/ -imaging technologies

Abstract The evolution of optical microscopy from an imaging technique into a tool for materials modification and fabrication is now being repeated with other characterization techniques, including scanning electron microscopy (SEM), focused ion beam (FIB) milling/imaging, and atomic force microscopy (AFM). Fabrication and in situ imaging of materials undergoing a three-dimensional (3D) nano-structuring within a 1−100 nm resolution window is required for future manufacturing of devices. This level of precision is critically in enabling the cross-over between different device platforms (e.g. from electronics to micro-/nano-fluidics and/or photonics) within future devices that will be interfacing with biological and molecular systems in a 3D fashion. Prospective trends in electron, ion, and nano-tip based fabrication techniques are presented.

Investigation of Ion Transmission Effects on Intact Protein Quantification in a Triple Quadrupole Mass Spectrometer.

Recently, direct intact protein quantitation using triple quadrupole mass spectrometry (QqQ-MS) and multiple reaction monitoring (MRM) was demonstrated (J. Am. Soc. Mass Spectrom. 27, 886-896 (2016)). Even though QqQ-MS is known to provide extraordinary detection sensitivity for quantitative analysis, we found that intact proteins exhibited a less than 5% ion transmission from the first quadrupole to the third quadrupole mass analyzer in the presence of zero collision energy (ZCE). With the goal to enhance intact protein quantitation sensitivity, ion scattering effects, proton transfer effects, and mass filter resolution widths were examined for their contributions to the lost signal. Protein standards myoglobin and ubiquitin along with small molecules reserpine and vancomycin were analyzed together with various collision induced dissociation (CID) gases (N2, He, and Ar) at different gas pressures. Mass resolution settings played a significant role in reducing ion transmission signal. By narrowing the mass resolution window by 0.35 m/z on each side, roughly 75%-90% of the ion signal was lost. The multiply charged proteins experienced additional proton transfer effects, corresponding to 10-fold signal reduction. A study of increased sensitivity of the method was also conducted with various MRM summation techniques. Although the degree of enhancement was analyte-dependent, an up to 17-fold increase in sensitivity was observed for ubiquitin using a summation of multiple MRM transitions. Biological matrix, human urine, and equine plasma were spiked with proteins to demonstrate the specificity of the method. This study provides additional insight into optimizing the use and sensitivity of QqQ-MS for intact protein quantification. Graphical Abstract ᅟ.

Rapid determination of 30 bioactive constituents in XueBiJing injection using ultra high performance liquid chromatography-high resolution hybrid quadrupole-orbitrap mass spectrometry coupled with principal component analysis

Xuebijing injection (XBJ) is a traditional Chinese herbal prescription widely used in the treatment of sepsis. Extensive chemical studies revealed that XBJ injection contains amino acids, phenolic acids, flavonoid glycosides, terpeneglycosides and phthalides. In this study, the applicability of ultra high performance liquid chromatography coupled with high resolution hybrid quadruple-orbitrap mass spectrometry (UHPLC-Q-Orbitrap MS) for the simultaneous quantitative analysis of 30 bioactive constituents in XueBiJing injection (XBJ) was investigated. The mass spectrometer was operated in full MS scan mode. The use of 70,000FWHM mass resolution and narrow mass windows (5ppm) could effectively improve the selectivity of the method. Separation was achieved on a Waters ACQUITY UPLC® HSS C18 column (2.1mm×100mm, 1.8μm) with a gradient mobile phase consisting of acetonitrile-water (containing 10mM ammonium acetate) at a flow rate of 0.2mL/min. Satisfactory linearity was achieved within wide linear range and all correlation coefficients (r) of analytes were more than 0.9996. The limits of detection (LODs) were in the range of 0.1180–27.82ng/mL for different analytes. The relative standard deviations (RSDs) of inter- and intra-day precisions were less than 3.0% and the recoveries of the assay were in the range of 98.5%–101.5%. The validated method was successfully applied for simultaneous determination of 30 bioactive compounds in XueBiJing injection from 10 batches samples by UHPLC-Q-Orbitrap MS within 10min. Moreover, the results were evaluated principal component analysis and two compounds might be the most important chemical markers for chemical quality control of XBJ injection. The novel Q-Orbitrap mass spectrometry has been proved to be a very promising and powerful tool for routine screening of bioactive compounds in traditional Chinese medicine injection, ensuring drug safety and public health.

A Study on Performance Verification for Remodeling of Existing Building with EnPI

In the present study, the performance verification for remodeling of existing building was conducted. The EnPI V4.0 which is issued from US DOE was applied for conduction of performance verification. The target building were remodeled four times from 2011 to 2016. The items of remodeling are consisted of passive and active items. The passive items are replacement from aging window to resolution window and installation of outer wall insulation panel. The active items are change from aging absorption chiller to high efficiency absorption chiller and replace from fluorescent light to LED light. Sum up the result, change from aging absorption chiller to high efficiency absorption chiller project has the highest energy saving. As the result of replacement for absorption chiller, 26.9 TOE was reduced annually. The replacement from aging window to resolution window and installation of outer wall insulation panel have the second highest energy saving. The effect of energy saving isn't big difference between active and passive technology. However, active technology can be considered as more effective to save the energy than passive technology in terms of efficiency.

Application of an ultrahigh-performance liquid chromatography coupled to quadrupole-orbitrap high-resolution mass spectrometry for the rapid screening, identification and quantification of illegal adulterated glucocorticoids in herbal medicines.

In this work, the ultrahigh-performance liquid chromatography quadrupole orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) was applied to the rapid screening, identification and quantification of the illegal adulterated glucocorticoids in herbal medicines. The mass spectrometer was operated in positive ion mode and Full MS/dd-MS2 (data-dependent MS2) mode, where selected ions were subjected to a dd-MS2 scan with given fragmentation energy following a Full MS scan. The application of 70 000 FWHM mass resolution and narrow mass windows (5ppm) effectively improve the selectivity of the method, and a single injection was sufficient to perform the simultaneous screening and identification/quantification of 14 glucocorticoids in 15min. The method validation including selectivity, sensitivity, calibration curve, accuracy, precision, recovery, matrix effect and stability were evaluated. The results of all analytes showed excellent linear relationship while all coefficient of determination (r2) were>0.9990 over wide concentration ranges (e.g., 5-1000ng/mL for hydrocortisone butyrate, r2=1.0000). The recoveries were in the range of 86.1-102.7%, while the matrix effects ranged from 95.8%-105.8%. Accuracies and precisions were performed. The intra- and inter-day accuracies ranged from 90.6% to 108.9%, while the intra- and inter-day precisions were in the range of 0.5% to 8.5%. Finally, the established method was employed to detect illegal adulterated glucocorticoids in herbal medicines. It will provide more reliable technical basis for the drug quality supervision department and ensure public health.

Breaking the Cycle of Unrestrained Presidential National Security Power

As a number of scholars have argued, constitutional and statutory limits have failed to constrain presidential national security power after 9/11 (Fisher 2012b; Pious 2011; Glennon 2015; Edelson 2016). Both the George W. Bush and Obama administrations have found ways around legal limitations on presidential power, while a generally acquiescent Congress has often failed to act and Supreme Court decisions aimed at setting limits have failed to have an effect.If this diagnosis is right – that presidential power has broken free of the rule of law and must be reined in – then what is the prescription? How is this problem to be resolved, and how can a balance be struck between the need for sufficient presidential power to defend national security and the need for meaningful legal restraints on power? This paper will consider specific proposals aimed at achieving these goals. I will consider the role various actors can play: (a) members of Congress, (b) the press, (c) the public, (d) scholars, (e) executive branch lawyers and (f) the courts. My methodological approach is qualitative, based on an analysis of specific actions taken by past presidents, other executive branch actors, legislators, and judges. I use primary sources, including executive orders, Department of Justice memoranda, and court decisions. I also draw on relevant scholarship in the area, including the sources mentioned above. For those interested in finding ways to limit presidential power, recent history provides hopeful examples, including (1) actions members of Congress took in August 2013 to prevent President Obama from acting unilaterally against the Assad regime; (2) actions by some executive branch lawyers in both the George W. Bush (Jack Goldsmith on warrantless surveillance) and Obama administrations (Caroline Krass on military action in Libya after the War Powers Resolution window closed) and (3) legislative changes to bulk metadata collection following the Snowden revelations regarding surveillance. Recent history also provides cautionary tales, or examples to be avoided — for example, Congress’s failure to act regarding ISIS, Harold Koh’s definition of hostilities under the War Powers Resolution, and John Yoo’s memos advancing the idea of an unconstrained unitary executive.With a new president taking office next year, this is a useful moment to consider what actions can be taken to break the cycle of unrestrained presidential power. This paper proposes a number of specific ideas designed to achieve this goal.

Abstract P1-02-02: A review of 66 consecutive patients investigated for mammographic abnormalities by digital tomosynthesis guided vacuum assisted breast biopsy

Abstract OBJECTIVE: Vacuum-assisted breast biopsy (VABB) has replaced surgical biopsy for the assessment of mammographic abnormalities that are not evident clinically and or on ultrasound examination. The aim of this study was to determine the indications for, and accuracy of, vacuum-assisted breast biopsy (VABB) performed using digital breast tomosynthesis (DBT) guidance. (Hologic® Dimensions, Affirm guidance and Eviva handsets). MATERIALS AND METHODS: Design: Retrospective medical record and histopathologic review. Patients and method: We introduced DBT guided VABB in June 2014 having previously investigated such patients using the prone table technique. This is a review of the first 66 consecutive patients investigated using this technique up to April 2105. The following information was reviewed: Indication for VABB, (mammographic classification M1-5, type of abnormality – calcifications/mass/distortion), complications of the procedure itself, (failure to complete, infection, haematoma), the result of the multidisciplinary team (MDT) review of imaging/pathologic correlation and the outcome for the patient. RESULTS: In one case it proved impossible to locate the lesion and this patient has been excluded from further analysis. The mean age of the patients was 57 years (30-80years). VABB was proposed for patients with lesions initially reported as highly suspicious (M5) 4 patients (6%), suspicious (M4) in 18 patients (28%), intermediate (M3) in 37 patients (57%) or benign (M2) in 6 patients (9%). Mean size of the lesion was 13mm (range 3-100mm). Forty-four patients (68%) presented with micro calcifications, 14 (21%) with distortions in and 7 (11%) with masses. There were no complications (infection or haematoma) that required further management following the procedure. Review by the MDT agreed that all biopsies were adequate and removed representative tissue from the lesion (No B1s). Review showed that the histology was benign and consistent in 30 (46%) patients all of whom were discharged to routine screening. 19 (29%) cases were reported as B3 (ADH, flat atypia, LCIS or ALH) in whom all the calcifications had been removed in 13 (20%) and the patients discharged and 6 (9%) went to open biopsy for residual calcifications all of whom were benign on final analysis. There was one (1.5%) radial scar reported as B4 that went to open excision and proved benign. 15 (23%) proved malignant (B5a, B5b) and went on to definitive treatment (with one patient entered into the LORIS low risk DCIS trial). The procedure is quicker, more accurate (related to the higher resolution and larger window of the receptor plate) and involves less radiation exposure (often involving only one DBT exposure) when compared to performing the same procedure on the Hologic Platinum prone table. CONCLUSION: DBT-guided VABB is an accurate, convenient and safe procedure. Citation Format: Munir A, Moalla A, Williams HR, Thomas D, Huws AM, Holt SD. A review of 66 consecutive patients investigated for mammographic abnormalities by digital tomosynthesis guided vacuum assisted breast biopsy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-02-02.

Dendrochronology and middle Miocene petrified oak: Modern counterparts and interpretation

This study reports the first successful statistical ‘crossdating’ among many ring width time series from petrified wood, thus providing a replicable continuous annual resolution window into tree growth and environmental influences during the middle Miocene. The petrified samples, of the genus Quercus, originated at the Stinking Water (SW) locality in Oregon, a Miocene-aged exposure associated with the Columbia River Basalts. 40AR/39AR dating on pillow basalt from the locality yielded a weighted Plateau Age of 13.79±0.09Ma placing the death of the trees at the end of the Langhian Stage of the Middle Miocene (15.97±0.05 to 13.65±0.05Ma), during the middle Miocene Climate Transition (MMCT). Ring width time series from 26 radii, 17 different trees, show significant intercorrelation. A Modified Coexistence Approach was applied to determine the likely climate range when the SW trees were growing. The modified approach included regression of site-mean ring width time series statistic values on estimated soil moisture for the site locations, using site-mean data from 126 modern Quercus sites from across the United States. Identification of highly significant linearities indicated strong relationships between ring width intercorrelation and soil moisture and ring width variability and soil moisture. Comparison of individual modern site-mean statistical values with values calculated for the SW locality suggests a mesic growing environment for the SW Quercus, with moderate temperatures. Geographic placement of modern Quercus sites with site-mean statistics similar to the SW values indicates a modern analogue in the eastern United States. Modern distributions of mesic species in the genera present at the SW locality suggest similarities with the central and southern Appalachian Mountains and the Ozark/Ouachita Mountains, indicating a mean annual temperature range of ≅10 °C to ≅15 °C and a mean annual precipitation range of ≅750 mm to ≅1200 mm when the SW Quercus were growing.

High noise correlation between the functionally connected neurons in emergent V1 microcircuits.

Neural correlations (noise correlations and cross-correlograms) are widely studied to infer functional connectivity between neurons. High noise correlations between neurons have been reported to increase the encoding accuracy of a neuronal population; however, low noise correlations have also been documented to play a critical role in cortical microcircuits. Therefore, the role of noise correlations in neural encoding is highly debated. To this aim, through multi-electrodes, we recorded neuronal ensembles in the primary visual cortex of anaesthetized cats. By computing cross-correlograms, we divulged the functional network (microcircuit) between neurons within an ensemble in relation to a specific orientation. We show that functionally connected neurons systematically exhibit higher noise correlations than functionally unconnected neurons in a microcircuit that is activated in response to a particular orientation. Furthermore, the mean strength of noise correlations for the connected neurons increases steeply than the unconnected neurons as a function of the resolution window used to calculate noise correlations. We suggest that neurons that display high noise correlations in emergent microcircuits feature functional connections which are inevitable for information encoding in the primary visual cortex.

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

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.

Theory of angular-dispersive, imaging hard-x-ray spectrographs

A spectrograph is an optical instrument that disperses photons of different energies into distinct directions and space locations, and images photon spectra on a position-sensitive detector. Spectrographs consist of collimating, angular dispersive, and focusing optical elements. Bragg reflecting crystals arranged in an asymmetric scattering geometry are used as the dispersing elements. A ray-transfer matrix technique is applied to propagate x-rays through the optical elements. Several optical designs of hard x-ray spectrographs are proposed and their performance is analyzed. Spectrographs with an energy resolution of 0.1 meV and a spectral window of imaging up to a few tens of meVs are shown to be feasible for inelastic x-ray scattering (IXS) spectroscopy applications. In another example, a spectrograph with a 1-meV spectral resolution and 85-meV spectral window of imaging is considered for Cu K-edge resonant IXS (RIXS).

Abstract A40: Development of a perfusion-based 3D human tri-culture breast microtumor

Abstract Background: The tumor microenvironment (TME) is a 3D, dynamic interaction between tumor and stromal cells, extracellular matrix, and soluble factors which can promote tumor progression and resistance to therapy. Significant efforts are being made to develop long-term in vitro TME models to study cancer biology, improve drug development, and guide clinical decisions. We have developed a cost-effective micro-bioreactor culture device which enables a wide variety of dynamic cellular and TME interactions that can be monitored with in situ, label free, and non-lytic microscopic analysis. Using the 3DKUBE™, we developed a 3D breast cancer model composed of MCF-7 cells and fibroblasts in segregated co-culture and identified a highly active PI3K inhibitor that had limited activity in 2D monoculture. Based on a more complex morphologic and functional 3D mammary gland model that incorporates multiple human primary cells including epithelial cells (HuMEC), mammary fibroblasts, and adipocytes, our long-term 3D perfused tri-culture breast cancer model is designed to evaluate drug response continuously using non-lytic analysis. We theorize that different breast cancer epithelial cells will be supported in a standard 3D stromal platform which supports mammary gland function. Herein, we describe the 3DKUBE™ modifications and early optimization of a defined stromal TME which supports HuMECs in 3D perfusion. Materials &amp; Methods: Primary human cells were used to optimize seeding conditions for silk fibroin scaffolds containing Matrigel™/collagen hydrogels, including, media composition, cellular ratios, flow rates, and analytical methods for the 3DKUBE™. Destructive analytical methods included morphology (H&amp;E), phenotype (histology), viability &amp; survival (CyQuant, TUNEL, Ki-67), and ER, PR, and casein expression (RT-PCR). Non-lytic assays included metabolism (resazurin reduction), cytotoxicity (LDH release), soluble biomarker expression (xMAP™), and two-photon emission fluorescence via multiphoton microscopy (MPM). Results: The 3DKUBE™ imaging window (1.25 mm thick with a refractive index of 1.590, transmittance (~90%) at wavelengths &amp;gt;290 nm) was replaced with a No. 1.5 glass, high resolution window allowing non-destructive, in situ microscopic imaging. MPM images obtained provided cellular detail (granularity, nuclear-cytoplasmic ratio, size). Optimization of the media conditions and cell numbers revealed that a tri-culture ratio of 1:1:1 was stable in the silk-Matrigel-collagen scaffold during prolonged static and perfusion culture in mixed media. Differentiation of adipocytes had to be performed separately from the tri-culture due to the cytotoxicity of the differentiation media to the epithelial cells. This was achieved via a serial seeding and differentiation method. Our initial drug studies revealed that cytotoxicity could be monitored over the course of a week by multiple methods, including LDH secretion, Presto blue, and CyQuant. Though non-specific drug binding (CPT-11) was seen in the complex 3D matrix, it did not materially impact total drug concentrations. Conclusions: Our current optimization results indicate our ability to grow a bioengineered 3D human breast tri-culture model under perfusion using the 3DKUBE™ while monitoring tissue structure, function, and drug response through both lytic and non-lytic methods. Future Development: The optimized perfused stroma will be used to develop ex vivo breast microtumors of clinically relevant subtypes (ER+, Her+, triple negative) validated against targeted agents. If validated, these 3D microtumors may be applied as predictive phenotypic screens to improve preclinical and clinical breast cancer drug development. Citation Format: Teresa M. DesRochers, Stephen Shuford, Terri F. Bruce, Matthew R. Gevaert, Chaitra Cheluvaraju, Irene Georgakoudi, David L. Kaplan, Davie E. Orr, Howland E. Crosswell. Development of a perfusion-based 3D human tri-culture breast microtumor. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr A40. doi:10.1158/1538-7445.CHTME14-A40