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Rapid Generation of Tandem Mass Spectrometry Reference Libraries Using Immediate Drop-on-Demand Liquid Handling Coupled to an Open Port Sampling Interface
In metabolomics, tandem MS (MS2) fragmentation libraries are important for the identification of unknown features, but generating these libraries takes many valuable hours of instrument and operator time. Here, an immediate droplet-on-demand/open port sampling interface was used to rapidly acquire tandem MS of standards arrayed in a 96-well plate format. A workflow was developed for automated, high-throughput control of MS2 library generation. Pure standard mass spectral libraries were collected on Orbitrap and Q-TOF mass spectrometers for 192 compounds using 6 different collision energies with a throughput of 4 and 7.8 s/spectrum, respectively. Libraries were acquired using different solvent additives, precursor adducts, and ion polarities.
Approaches for handling high-dimensional cluster expansions of ionic systems
Disordered multicomponent systems attract great interest due to their engineering design flexibility and subsequent rich space of properties. However, detailed characterization of the structure and atomic correlations remains challenging and hinders full navigation of these complex spaces. A lattice cluster expansion is one tool to obtain configurational and energetic resolution. While in theory a cluster expansion can be applied to any system of any dimensionality, the method has primarily been used in binary systems or ternary alloys. Here we apply cluster expansions in high-component ionic systems, setting up the largest cluster expansion ever attempted to our knowledge. In doing so, we address and discuss challenges specific to high-component ionic systems, namely charge state assignments, structural relaxations, and rank-deficient systems. We introduce practical procedures to make the fitting and analysis of complex systems tractable, providing guidance for future computational studies of disordered ionic systems.
Design of robot grippers for binder jet products handling
Dimension accuracy, damage minimization, and defect detection are essential in manufacturing processes, especially additive manufacturing. These types of challenges may arise either during the manufacture of a product or its use. The repeatability of the process is vital in additive manufacturing systems. However, human users may lose concentration and, thus, would be a great alternative as an assistant. Depending on the nature of work, a robot’s fingers might vary, for example, mechanical, electrical, vacuum, two-fingers, and three-fingers. In addition, the end effector plays a vital role in picking up an object in the advanced manufacturing process. However, inbuilt robotic fingers may not be appropriate in different production environments. In this research presented here considering metal binder jet additive manufacturing, the two-finger end- effectors are proposed design, analysis, and experiment to pick up an object after completing the production process from a specific location. The final designs were further printed by using a 3D metal printer and installed in the existing robotic systems. These new designs are used successfully to hold the object from the specific location by reducing the contact force that was not possible with the previously installed end effector's finger. In addition, a numerical study was conducted in order to compare the flowability of the geometric shape of finger's free areas.
Handling radiation generated during an ion source commissioning
Radiation is an important issue, which should be carefully treated during the design and commissioning of an ion source. Measurements show that X-rays are generated around the ceramics column of an extraction system when the source is powered up to 30 kV. The X-ray dose increases greatly when a beam is extracted. Inserting the ceramic column into a metal vacuum box is a good way to block X-ray emission for those cases. Moreover, this makes the online test of an intense H{sup +} ion beam with energy up to 100 keV possible. However, for deuteron ion source commissioning, neutron and gamma-ray radiation become a serious topic. In this paper, we will describe the design of the extraction system and the radiation doses of neutrons and gamma-rays measured at different D{sup +} beam energy during our 2.45 GHz deuteron electron cyclotron resonance ion source commissioning for PKUNIFTY (PeKing University Neutron Imaging FaciliTY) project at Peking University.
A method for data handling numerical results in parallel OpenFOAM simulations
Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit{sup ®}[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.
Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR
We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization ({sup RESPIRATION}CP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the {sup RESPIRATION}CP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous {sup 15}N → {sup 13}CO and {sup 15}N → {sup 13}C{sub α} coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.
Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism
Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions1-3. Different families of enzymes, known as peptidyl-prolyl isomerases (PPIases), catalyse this reaction, which involves the interconversion between the cis and trans isomers of the Nterminal amide bond of the amino acid proline2,3. A complete description of the mechanisms by which these enzymes function, however, has remained elusive. Here, we show that cyclophilin A, one of the most common PPIases4, provides a catalytic environment that acts on the substrate through an electrostatic lever mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carboxylic group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. This mechanism resulted from the analysis of an ensemble of conformations populated by cyclophilin A during the enzymatic reaction using a combination of NMR measurements, molecular dynamics simulations and density functional theory calculations. We anticipate that this approach will be helpful in elucidating whether the electrostatic lever mechanism that we describe is common to other PPIases, and more generally to characterise other enzymatic processes.
Diagnostic Technique Characterizing Neutron Irradiation Effects on Additively Manufactured Inconel 625 Eliminating the Need for Remote Handling
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LCLS Big Data Handling – How I Learned to Stop Worrying and Love the Data Deluge
Advanced data and computing systems are vital to Linac Coherent Light Source (LCLS) operations, data interpretation and overall scientific productivity. The transition to MHz-era operation marks a fundamental change in scale that requires new infrastructure and architectures to link LCLS to the required scale of computing needed for scientific interpretation. The LCLS-II Data System meets big data challenges by implementing configurable data reduction that can adapt to multiple science areas, real-time analysis frameworks to provide visualization and fast feedback, and the ability to transfer data to local and remote computational facilities for near real time analysis at the appropriate scale. Feature extracted information generated in the data analysis pipeline - at the edge, local compute, or remote High-Performance Computing (HPC) resources - can be used to steer experiments and inform user decisions during beam time. Artificial Intelligence and Machine Learning (AI/ML) techniques present new opportunities to rapidly analyse large datasets and direct experiments, but create new challenges in scaling, adaptability, complexity, and trustworthiness. We describe how the LCLS-II Data System architecture addresses its data-driven challenges in the areas of data acquisition, data processing, data management, and workflow orchestration to decrease the overall time-to-science and provide a vision for future developments.
Prospects for Disruption Handling in a Tokamak-Based Fusion Reactor
Not provided.
Development of high-fidelity air handling unit fault models for FDD innovation: lessons learned and recommendations
Not Available
High performance power handling in the absence of an H-mode edge in negative triangularity DIII-D plasmas
Abstract Experiments performed during strongly-shaped high-power diverted negative triangularity (NT) experiments in DIII-D achieved detached divertor conditions and a transient-free edge, showcasing the potential for application of NT to a core-edge integrated reactor-like scenario and providing the first characterization of the parametric dependencies for detachment onset. Detached divertor conditions will be required in future devices to mitigate divertor heat fluxes. Access to dissipative divertor conditions was investigated via an increase in upstream density. Detachment onset at the outer strike point was achieved with H-mode level confinement H 98 − y 2 ∼ 1 and reactor-relevant normalized pressures β N ∼ 2 . Confinement degradation was observed with deeper detachment, associated with the loss of an electron temperature pedestal. Differences in geometry, radial transport, impact of cross field drifts are discussed to explain differences in access to detachment in NT discharges. Higher normalized densities, with respect to equivalent discharges in positive triangularity, were necessary to achieve detachment, partially explained by the shorter parallel connection length to the targets. The effect of cross-field particle drifts ( E × B , B × ∇ B ) on access to detachment was demonstrated by the lower upstream density needed to access detachment with ion B × ∇ B drift directed outside of the active divertor (Greenwald fraction f Gw ∼ 0.9–1.0 vs f Gw ∼ 1.3). The upstream density at detachment onset was observed to increase linearly with plasma current with ion B × ∇ B drift into the divertor, consistent with the observed narrowing of the scrape-off layer heat flux width λ q . Edge fluid simulations capture separatrix densities needed to achieve detachment in NT plasma and their dependence on drift direction. The ability to reproduce detachment dynamics in NT plasma increases the confidence in future design studies for NT divertors.
Online Data Handling and Storage at the CMS Experiment
During the LHC Long Shutdown 1, the CMS Data Acquisition (DAQ) system underwent a partial redesign to replace obsolete network equipment, use more homogeneous switching technologies, and support new detector back-end electronics. The software and hardware infrastructure to provide input, execute the High Level Trigger (HLT) algorithms and deal with output data transport and storage has also been redesigned to be completely file- based. All the metadata needed for bookkeeping are stored in files as well, in the form of small documents using the JSON encoding. The Storage and Transfer System (STS) is responsible for aggregating these files produced by the HLT, storing them temporarily and transferring them to the T0 facility at CERN for subsequent offline processing. The STS merger service aggregates the output files from the HLT from ~62 sources produced with an aggregate rate of ~2GB/s. An estimated bandwidth of 7GB/s in concurrent read/write mode is needed. Furthermore, the STS has to be able to store several days of continuous running, so an estimated of 250TB of total usable disk space is required. In this article we present the various technological and implementation choices of the three components of the STS: the distributed file system, the merger service and the transfer system.
miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources
Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.
Pulse profile modelling of thermonuclear burst oscillations – II. Handling variability
ABSTRACT Pulse profile modelling is a relativistic ray-tracing technique that can be used to infer masses, radii, and geometric parameters of neutron stars. In a previous study, we looked at the performance of this technique when applied to thermonuclear burst oscillations from accreting neutron stars. That study showed that ignoring the variability associated with burst oscillation sources resulted in significant biases in the inferred mass and radius, particularly for the high count rates that are nominally required to obtain meaningful constraints. In this follow-on study, we show that the bias can be mitigated by slicing the bursts into shorter segments where variability can be neglected, and jointly fitting the segments. Using this approach, the systematic uncertainties on the mass and radius are brought within the range of the statistical uncertainty. With about 106 source counts, this yields uncertainties of approximately 10 per cent for both the mass and radius. However, this modelling strategy requires substantial computational resources. We also confirm that the posterior distributions of the mass and radius obtained from multiple bursts of the same source can be merged to produce outcomes comparable to that of a single burst with an equivalent total number of counts.