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At least 1,567 records · Page 87

High-performance data management for whole slide image analysis in digital pathology

When dealing with giga-pixel digital pathology in whole-slide imaging, a notable proportion of data records holds relevance during each analysis operation. For instance, when deploying an image analysis algorithm on whole-slide images (WSI), the computational bottleneck often lies in the input-output (I/O) system. This is particularly notable as patch-level processing introduces a considerable I/O load onto the computer system. However, this data management process could be further paralleled, given the typical independence of patch-level image processes across different patches. This paper details our endeavors in tackling this data access challenge by implementing the Adaptable IO System version 2 (ADIOS2). Our focus has been constructing and releasing a digital pathology-centric pipeline using ADIOS2, which facilitates streamlined data management across WSIs. Additionally, we’ve developed strategies aimed at curtailing data retrieval times. The performance evaluation encompasses two key scenarios: (1) a pure CPU-based image analysis scenario (“CPU scenario”), and (2) a GPU-based deep learning framework scenario (“GPU scenario”). Our findings reveal noteworthy outcomes. Under the CPU scenario, ADIOS2 showcases an impressive two-fold speed-up compared to the brute-force approach. In the GPU scenario, its performance stands on par with the cutting-edge GPU I/O acceleration framework, NVIDIA Magnum IO GPU Direct Storage (GDS). From what we know, this appears to be among the initial instances, if any, of utilizing ADIOS2 within the field of digital pathology. The source code has been made publicly available at https://github.com/hrlblab/adios.

Wang, Xiao↗

Monte Carlo simulations of patient dose perturbations in rotational-type radiotherapy due to a transverse magnetic field: A tomotherapy investigation

Purpose: Several groups are exploring the integration of magnetic resonance (MR) image guidance with radiotherapy to reduce tumor position uncertainty during photon radiotherapy. The therapeutic gain from reducing tumor position uncertainty using intrafraction MR imaging during radiotherapy could be partially offset if the negative effects of magnetic field-induced dose perturbations are not appreciated or accounted for. The authors hypothesize that a more rotationally symmetric modality such as helical tomotherapy will permit a systematic mediation of these dose perturbations. This investigation offers a unique look at the dose perturbations due to homogeneous transverse magnetic field during the delivery of Tomotherapy{sup ®} Treatment System plans under varying degrees of rotational beamlet symmetry. Methods: The authors accurately reproduced treatment plan beamlet and patient configurations using the Monte Carlo code GEANT4. This code has a thoroughly benchmarked electromagnetic particle transport physics package well-suited for the radiotherapy energy regime. The three approved clinical treatment plans for this study were for a prostate, head and neck, and lung treatment. The dose heterogeneity index metric was used to quantify the effect of the dose perturbations to the target volumes. Results: The authors demonstrate the ability to reproduce the clinical dose–volume histograms (DVH) to within 4% dose agreement at each DVH point for the target volumes and most planning structures, and therefore, are able to confidently examine the effects of transverse magnetic fields on the plans. The authors investigated field strengths of 0.35, 0.7, 1, 1.5, and 3 T. Changes to the dose heterogeneity index of 0.1% were seen in the prostate and head and neck case, reflecting negligible dose perturbations to the target volumes, a change from 5.5% to 20.1% was observed with the lung case. Conclusions: This study demonstrated that the effect of external magnetic fields can be mitigated by exploiting a more rotationally symmetric treatment modality.

60 APPLIED LIFE SCIENCES↗

Conflation of Geospatial POI Data and Ground-level Imagery

The code solves the problem of conflating POI (Points of Interest) geospatial data and geo-tagged ground-level imagery data. The main challenges with fusion or conflation of these two types of data has been that these two data entities are represented not only in several ways in current state-of-the-art, but also there is mismatch of representation format of these two data types. This source code/software brings POI datapoints and ground-level imagery datapoints into same representation format, and then generates valuable Knowledge Graph combining POI and images data (so that it can be used for multitude of applications).

De, Debraj↗

Calculation of photodetachment cross sections and photoelectron angular distributions of negative ions using density functional theory

Recently, the development of photoelectron velocity map imaging makes it much easier to obtain the photoelectron angular distributions (PADs) experimentally. However, explanations of PADs are only qualitative in most cases, and very limited works have been reported on how to calculate PAD of anions. In the present work, we report a method using the density-functional-theory Kohn-Sham orbitals to calculate the photodetachment cross sections and the anisotropy parameter β. The spherical average over all random molecular orientation is calculated analytically. A program which can handle both the Gaussian type orbital and the Slater type orbital has been coded. The testing calculations on Li{sup −}, C{sup −}, O{sup −}, F{sup −}, CH{sup −}, OH{sup −}, NH{sub 2}{sup −}, O{sub 2}{sup −}, and S{sub 2}{sup −} show that our method is an efficient way to calculate the photodetachment cross section and anisotropy parameter β for anions, thus promising for large systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

THE EFFECT OF MAGNETIC TOPOLOGY ON THERMALLY DRIVEN WIND: TOWARD A GENERAL FORMULATION OF THE BRAKING LAW

Stellar wind is thought to be the main process responsible for the spin down of main-sequence stars. The extraction of angular momentum by a magnetized wind has been studied for decades, leading to several formulations for the resulting torque. However, previous studies generally consider simple dipole or split monopole stellar magnetic topologies. Here we consider, in addition to a dipolar stellar magnetic field, both quadrupolar and octupolar configurations, while also varying the rotation rate and the magnetic field strength. Sixty simulations made with a 2.5D cylindrical and axisymmetric set-up, and computed with the PLUTO code, were used to find torque formulations for each topology. We further succeed to give a unique law that fits the data for every topology by formulating the torque in terms of the amount of open magnetic flux in the wind. We also show that our formulation can be applied to even more realistic magnetic topologies, with examples of the Sun in its minimum and maximum phases as observed at the Wilcox Solar Observatory, and of a young K-star (TYC-0486-4943-1) whose topology has been obtained by Zeeman-Doppler Imaging.

79 ASTRONOMY AND ASTROPHYSICS↗

A steady-state picture of solar wind acceleration and charge state composition derived from a global wave-driven MHD model

The higher charge states found in slow (<400 km s{sup −1}) solar wind streams compared to fast streams have supported the hypothesis that the slow wind originates in closed coronal loops and is released intermittently through reconnection. Here we examine whether a highly ionized slow wind can also form along steady and open magnetic field lines. We model the steady-state solar atmosphere using the Alfvén Wave Solar Model (AWSoM), a global MHD model driven by Alfvén waves, and apply an ionization code to calculate the charge state evolution along modeled open field lines. This constitutes the first charge state calculation covering all latitudes in a realistic magnetic field. The ratios O{sup +7}/O{sup +6} and C{sup +6}/C{sup +5} are compared to in situ Ulysses observations and are found to be higher in the slow wind, as observed; however, they are underpredicted in both wind types. The modeled ion fractions of S, Si, and Fe are used to calculate line-of-sight intensities, which are compared to Extreme-ultraviolet Imaging Spectrometer (EIS) observations above a coronal hole. The agreement is partial and suggests that all ionization rates are underpredicted. Assuming the presence of suprathermal electrons improved the agreement with both EIS and Ulysses observations; importantly, the trend of higher ionization in the slow wind was maintained. The results suggest that there can be a sub-class of slow wind that is steady and highly ionized. Further analysis shows that it originates from coronal hole boundaries (CHBs), where the modeled electron density and temperature are higher than inside the hole, leading to faster ionization. This property of CHBs is global and observationally supported by EUV tomography.

79 ASTRONOMY AND ASTROPHYSICS↗

Staged Z-pinch experiment at the double-EAGLE pulsed power facility

The staged Z-pinch is a potential high-energy gain fusion concept where a high atomic number liner implodes on a deuterium target using a pulsed multi-MA current source. Over the past several years this concept has been studied on 0.5–1.0 MA facilities using Ar and Kr gas puffs injected at R = 1.2 cm. Neutron yield up to (2.5 ± 0.34) x 10 10 was measured, Ruskov et al (2023 IEEE Trans. Plasma Sci. 51 3310–6). Here, in this study, we present experimental results from the 4 MA, 110 ns current rise time Double-EAGLE facility at L3Harris (currently, Fisica Inc.) where a larger radius nozzle created gas density profiles peaked at R = 2.5 cm. Modeling with the MACH2 and FLASH codes indicates that the larger radius allows stronger acceleration of the liner plasma and generation of shock waves that preheat a target plasma layer next to the liner to temperatures $T_i >$1 keV. The resulting counter thermal pressure on the liner plasma limits the growth of the Magneto-Rayleigh–Taylor (MRT) instability at the liner-vacuum boundary and the implosion proceeds in a relatively stable manner. Near bang time the enormous target plasma thermal pressure smoothens the MRT perturbations developed during the earlier implosion stages. Time integrated x-ray pinhole images with cutoff energy of 100 eV confirm that a long (∼3 cm), stable and uniform high energy density plasma column is formed in the final implosion stage. Consistent neutron yield in the 10 10 –10 11 range was measured for both Ar and Kr liners imploding on a deuterium target.

Physics - Plasma physics↗

Probe microscopy is all you need *

We pose that microscopy offers an ideal real-world experimental environment for the development and deployment of active Bayesian and reinforcement learning methods. Indeed, the tremendous progress achieved by machine learning (ML) and artificial intelligence over the last decade has been largely achieved via the utilization of static data sets, from the paradigmatic MNIST to the bespoke corpora of text and image data used to train large models such as GPT3, DALL·E and others. However, it is now recognized that continuous, minute improvements to state-of-the-art do not necessarily translate to advances in real-world applications. We argue that a promising pathway for the development of ML methods is via the route of domain-specific deployable algorithms in areas such as electron and scanning probe microscopy and chemical imaging. This will benefit both fundamental physical studies and serve as a test bed for more complex autonomous systems such as robotics and manufacturing. Favorable environment characteristics of scanning and electron microscopy include low risk, extensive availability of domain-specific priors and rewards, relatively small effects of exogenous variables, and often the presence of both upstream first principles as well as downstream learnable physical models for both statics and dynamics. Recent developments in programmable interfaces, edge computing, and access to application programming interfaces (APIs) facilitating microscope control, all render the deployment of ML codes on operational microscopes straightforward. We discuss these considerations and hope that these arguments will lead to create novel set of development targets for the ML community by accelerating both real world ML applications and scientific progress.

47 OTHER INSTRUMENTATION↗

TU-EF-204-09: A Preliminary Method of Risk-Informed Optimization of Tube Current Modulation for Dose Reduction in CT

Purpose: X-rays from CT scans can increase cancer risk to patients. Lifetime Attributable Risk of Cancer Incidence for adult patients has been investigated and shown to decrease as patient age. However, a new risk model shows an increasing risk trend for several radiosensitive organs for middle age patients. This study investigates the feasibility of a general method for optimizing tube current modulation (TCM) functions to minimize risk by reducing radiation dose to radiosensitive organs of patients. Methods: Organ-based TCM has been investigated in literature for eye lens dose and breast dose. Adopting the concept in organ-based TCM, this study seeks to find an optimized tube current for minimal total risk to breasts and lungs by reducing dose to these organs. The contributions of each CT view to organ dose are determined through simulations of CT scan view-by-view using a GPU-based fast Monte Carlo code, ARCHER. A Linear Programming problem is established for tube current optimization, with Monte Carlo results as weighting factors at each view. A pre-determined dose is used as upper dose boundary, and tube current of each view is optimized to minimize the total risk. Results: An optimized tube current is found to minimize the total risk of lungs and breasts: compared to fixed current, the risk is reduced by 13%, with breast dose reduced by 38% and lung dose reduced by 7%. The average tube current is maintained during optimization to maintain image quality. In addition, dose to other organs in chest region is slightly affected, with relative change in dose smaller than 10%. Conclusion: Optimized tube current plans can be generated to minimize cancer risk to lungs and breasts while maintaining image quality. In the future, various risk models and greater number of projections per rotation will be simulated on phantoms of different gender and age. National Institutes of Health R01EB015478.

60 APPLIED LIFE SCIENCES↗

MCR Container Tools

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting from them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.

Haas, NicholasQ↗

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting

Many existing object counting methods rely on density map estimation (DME) of the discrete grid representation by decoding extracted image semantic features from designed convolutional neural networks (CNNs). Relying on discrete density maps not only leads to information loss dependent on the original image resolution, but also has a scalability issue when analyzing high-resolution images with cubically increasing memory complexity. Furthermore, none of the existing methods can offer reliable uncertainty quantification (UQ) for the derived count estimates. To overcome these limitations, we design UNcertainty-aware, hypernetwork-based Implicit neural representations for Counting (UNIC) to assign probabilities and the corresponding counting confidence over continuous spatial coordinates. We derive a sampling-based Bayesian counting loss function and develop the corresponding model training algorithm. UNIC outperforms existing methods on the Remote Sensing Object Counting (RSOC) dataset with reliable UQ and improved interpretability of the derived count estimates. Our code is available at https://github.com/SiyuanXu-tamu/UNIC.

97 MATHEMATICS AND COMPUTING↗

Multi-institutional Feasibility Study of a Fast Patient Localization Method in Total Marrow Irradiation With Helical Tomotherapy: A Global Health Initiative by the International Consortium of Total Marrow Irradiation

Purpose: To develop, characterize, and implement a fast patient localization method for total marrow irradiation. Methods and Materials: Topographic images were acquired using megavoltage computed tomography (MVCT) detector data by delivering static orthogonal beams while the couch traversed through the gantry. Geometric and detector response corrections were performed to generate a megavoltage topogram (MVtopo). We also generated kilovoltage topograms (kVtopo) from the projection data of 3-dimensional CT images to reproduce the same geometry as helical tomotherapy. The MVtopo imaging dose and the optimal image acquisition parameters were investigated. A multi-institutional phantom study was performed to verify the image registration uncertainty. Forty-five MVtopo images were acquired and analyzed with in-house image registration software. Results: The smallest jaw size (front and backup jaws of 0) provided the best image contrast and longitudinal resolution. Couch velocity did not affect the image quality or geometric accuracy. The MVtopo dose was less than the MVCT dose. The image registration uncertainty from the multi-institutional study was within 2.8 mm. In patient localization, the differences in calculated couch shift between the registration with MVtopo-kVtopo and MVCT-kVCT images in lateral, cranial–caudal, and vertical directions were 2.2 ± 1.7 mm, 2.6 ± 1.4 mm, and 2.7 ± 1.1 mm, respectively. The imaging time in MVtopo acquisition at the couch speed of 3 cm/s was <1 minute, compared with ≥15 minutes in MVCT for all patients. Conclusion: Whole-body MVtopo imaging could be an effective alternative to time-consuming MVCT for total marrow irradiation patient localization.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An evaluation of the contouring abilities of medical dosimetry students for the anatomy of a prostate cancer patient

Prostate cancer is one of the most common diseases treated in a radiation oncology department. One of the major predictors of the treatment outcome and patient side effects is the accuracy of the anatomical contours for the treatment plan. Therefore, the purpose of this study was to determine which anatomical structures are most often contoured correctly and incorrectly by medical dosimetry students. The author also wanted to discover whether a review of the contouring rules would increase contouring accuracy. To achieve this, a male computed tomography dataset consisting of 72 transverse slices was sent to students for contouring. The students were instructed to import this dataset into their treatment planning system and contour the following structures: skin, bladder, rectum, prostate, penile bulb, seminal vesicles, left femoral head, and right femoral head. Upon completion of the contours, the contour file was evaluated against a 'gold standard' contour set using StructSure software (Standard Imaging, Inc). A review of the initial contour results was conducted and then students were instructed to contour the dataset a second time. The results of this study showed significant differences between contouring sessions. These results and the standardization of contouring rules should benefit all individuals who participate in the treatment planning of cancer patients.

61 RADIATION PROTECTION AND DOSIMETRY↗

SU-C-201-07: Validation of a GATE Gamma Camera Model for the Siemens Symbia

Purpose: To develop a simulation model of a clinical gamma camera/SPECT system and to validate the model using experimental and published measurements from the clinical system. Methods: Geant4 Application for Tomographic Emission (GATE) was used to create a model of the Siemens Symbia gamma camera. A modular model was implemented that allows specifying combinations of crystal thickness (3/8”, 5/8”) and collimator (LEHR, MELP, HE). Shielding, energy resolution, intrinsic resolution, crystal thickness, and collimator properties were set based on manufacturer specifications. Validation of the model was performed by simulating NEMA 2007 gamma camera tests including spatial resolution and sensitivity for Tc99; these were compared with experimental and published data for the scanner. The simulated energy spectra of a Tc99 line source in acrylic blocks was visually compared with the corresponding experimental acquisition. For a 4 cm diameter sphere filled with Tc99, the attenuation maps were generated from simulation data, and the photopeak and scatter window were extracted from GATE output using ROOT to create DICOM files to use in the clinical reconstruction. Results: Simulated spatial resolutions for LEHR 3/8” crystal at 0, 10 cm, 10 cm (with scatter), and 30 cm were 4, 6.7, 7.9, and 14.5 mm FWHM; these were 9% less than published data. For 5/8” crystal the spatial resolutions were 4.5, 7.0, 8.5, and 14.7 mm FWHM; these were 4% to 10% less than published data. Simulated sensitivity was within 3.5% of published data for both LEHR 3/8” and 5/8”. The simulated energy spectra matched the photopeak and scatter window well, but did overestimate the counts below 90 keV. The simulated attenuation map and projection data were successfully reconstructed with the clinical software, and the passed visual inspection. Conclusions: Validation of a specific clinical scanner allows future studies of quantification accuracy for both planar and SPECT imaging. Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under Award Number R01CA138986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

60 APPLIED LIFE SCIENCES↗

TU-FG-201-03: Automatic Pre-Delivery Verification Using Statistical Analysis of Consistencies in Treatment Plan Parameters by the Treatment Site and Modality

Purpose: A novel computer software system, namely APDV (Automatic Pre-Delivery Verification), has been developed for verifying patient treatment plan parameters right prior to treatment deliveries in order to automatically detect and prevent catastrophic errors. Methods: APDV is designed to continuously monitor new DICOM plan files on the TMS computer at the treatment console. When new plans to be delivered are detected, APDV checks the consistencies of plan parameters and high-level plan statistics using underlying rules and statistical properties based on given treatment site, technique and modality. These rules were quantitatively derived by retrospectively analyzing all the EBRT treatment plans of the past 8 years at authors’ institution. Therapists and physicists will be notified with a warning message displayed on the TMS computer if any critical errors are detected, and check results, confirmation, together with dismissal actions will be saved into database for further review. Results: APDV was implemented as a stand-alone program using C# to ensure required real time performance. Mean values and standard deviations were quantitatively derived for various plan parameters including MLC usage, MU/cGy radio, beam SSD, beam weighting, and the beam gantry angles (only for lateral targets) per treatment site, technique and modality. 2D-based rules of combined MU/cGy ratio and averaged SSD values were also derived using joint probabilities of confidence error ellipses. The statistics of these major treatment plan parameters quantitatively evaluate the consistency of any treatment plans which facilitates automatic APDV checking procedures. Conclusion: APDV could be useful in detecting and preventing catastrophic errors immediately before treatment deliveries. Future plan including automatic patient identify and patient setup checks after patient daily images are acquired by the machine and become available on the TMS computer. This project is supported by the Agency for Healthcare Research and Quality (AHRQ) under award 1R01HS0222888. The senior author received research grants from ViewRay Inc. and Varian Medical System.

60 APPLIED LIFE SCIENCES↗

G305.136+0.068: A MASSIVE AND DENSE COLD CORE IN AN EARLY STAGE OF EVOLUTION

We report molecular line observations, made with ASTE and SEST, and dust continuum observations at 0.87 mm, made with APEX, toward the cold dust core G305.136+0.068. The molecular observations show that the core is isolated and roughly circularly symmetric and imply that it has a mass of 1.1 × 10{sup 3} M {sub ☉}. A simultaneous model fitting of the spectra observed in four transitions of CS, using a non-LTE radiative transfer code, indicates that the core is centrally condensed, with the density decreasing with radius as r {sup –1.8}, and that the turbulent velocity increases toward the center. The dust observations also indicate that the core is highly centrally condensed and that the average column density is 1.1 g cm{sup –2}, a value slightly above the theoretical threshold required for the formation of high-mass stars. A fit to the spectral energy distribution of the emission from the core indicates a dust temperature of 17 ± 2 K, confirming that the core is cold. Spitzer images show that the core is seen in silhouette from 3.6 to 24.0 μm and that it is surrounded by an envelope of emission, presumably tracing an externally excited photo-dissociated region. We found two embedded sources within a region of 20'' centered at the peak of the core, one of which is young, has a luminosity of 66 L {sub ☉}, and is accreting mass with a high accretion rate of ∼1 × 10{sup –4} M {sub ☉} yr{sup –1}. We suggest that this object corresponds to the seed of a high-mass protostar still in the process of formation. The present observations support the hypothesis that G305.136+0.068 is a massive and dense cold core in an early stage of evolution, in which the formation of a high-mass star has just started.

79 ASTRONOMY AND ASTROPHYSICS↗

Overview on Shielding Analyses for the VENUS Instrument at SNS

VENUS, a world‐class versatile neutron imaging instrument, is under construction and is expected to be completed and ready to start commissioning in 2023. The range of cold to epithermal neutrons at SNS will give users of VENUS access to novel imaging methods, as well as to significantly improved existing methods. The instrument is being built on beam line 10 at Spallation Neutron Source (SNS) First Target Station (FTS) facing a decoupled poisoned hydrogen moderator. Instrument design, which includes optics, Front-End components and instrument enclosure components and shape started over 10 years ago and during this time had significant changes. All changes were supported by neutronics analyses to provide adequate shielding for both Front-End and instrument enclosure.Final optics design will provide the field of view (FOV) at the detector position (where the image is formed) to be as high as 0.20 by 0.20 m. Both the beam, which contains a large fraction of high-energy neutrons, and the desire for a large footprint on the detector are challenges for shielding design and budget, because the driving cost for the instrument is the beam line and enclosure shielding. For cost reason VENUS baseline design is optimized with respect to both the instrument cave footprint and its wall thickness, and Front-End shielding is tailored along the beam. Analyses are performed with the Monte Carlo particle transport code MCNPX version 2.7.0 to make choices on materials, thicknesses and configurations of the shielding. Numerous calculations are performed to meet space and coast constrain and to satisfy instrument physics needs and to comply with radiation protection requirements.

Gallmeier, Franz X.↗

Using extended MHD to explore lasers as a trigger for x-pinches

X-pinches have been shown to be a source of extremely intense x-ray emissions useful for diagnosing plasma dynamics and imaging biological objects. The most striking feature of an x-pinch is the hotspot, the point source from where all the x rays come from. Unfortunately, the exact timing and location of the hotspot are still unpredictable. Since an x-pinch hotspot forms from instabilities (like an m = 0 mode), we will computationally explore whether we can use a high-power laser to control the timing and location of these instabilities. Our goal is to reduce the temporal and spatial jitter associated with the x-ray burst. Using an extended MHD (XMHD) code, we explore the non-relativistic instability generation using a current profile of a 250 kA linear transformer driver system and laser characteristics of SLAC's Matter in Extreme Conditions laboratory. Our results include both laser-penetration results using a boundary-defined electromagnetic (EM) wave and instability results from a power-deposition method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗