gebhart/patrepeval huggingface dataset:
SU‐FF‐J‐73: Treatment Simulation for 4D Image Guided Radiation Therapy (2005)

Purpose: To investigate the feasibility of a dynamic treatment simulation system, PortSim ± for four‐dimensional image guided radiation therapy (4DIGRT) and respiratory gated Intensity Modulated Radiation Therapy (RGIMRT). Method and Materials: PortSim± is an in‐house developed software package that allows for simulation of 4DIGRT and RGIMRT. The software is integrated with our conventional simulator. Prior to simulation, a set of DRRs at different respiration phases along with the corresponding anatomic contours were imported from the treatment planning station. The respiratory rhythm and cycle of the patient is captured using a radio‐opaque marker which reflects the circumference change of a binding belt around patient's chest. The marker correlates with the respiratory cycle and can be easily detected. In 4DIGRT simulation, the displayed reference DRR and corresponding MLC is triggered by the respiratory cycle. Similarly for RGIMRT, the MLC overlay is linked to the respiration phase and duty cycle threshold. Once the dynamic MLC characteristics are accounted for, both 4DIGRT and RGIMRT can be simulated prior to delivery in order to ensure that patient is positioned accurately and the treatment is delivered as planned. Results: PortSim ± incorporates live acquisition of high quality fluoroscopic images (1024 × 1024), image intensifier distortion correction, breathing phase detection, reference DRRs and MLC display. The software runs on a Pentium IV 2.2 GHz, with 1G RAM computer. Initial results show that the system can successfully detect the breathing cycle and sequence the display and superposition of DRRs and dMLC. The complete simulation can be recorded at a rate of 30 frames per second for later review and analysis. Conclusion: The initial experience with this system indicates that uncertainties in set‐up and delivery of 4DIGRT and RGIMRT treatment can be greatly reduced. The recorded simulation provides information that could influence field design and plan development.
Endotoxin-Neutralizing Peptides as Gram-Negative Sepsis Therapeutics (2009)

Bacterial endotoxin [e.g. lipopolysaccharide (LPS)] can trigger systemic hyper-inflammatory that subsequently leads to multiple organ failure and lethality (gram-negative sepsis). This paper describes the development of endotoxinneutralizing peptides that potentially treat sepsis. These peptides have been derived from bactericidal/permeabilityincreasing protein (BPIP), anti-microbial peptides, and leukocyte CD18 antigen and some of these peptides have been tested in clinical studies. Keywords: Endotoxin-neutralizing peptide, BPIP, anti-microbial peptide, CD18, gram-negative sepsis
Synthesis of 2‐and 6‐chloro‐3‐(5‐methyl‐1,3,4‐oxadiazol‐2‐yl)pyridines (1980)

Abstract A convenient synthesis of 2‐ and 6‐chloro‐3‐(5‐methyl‐1,3,4‐oxadiazol‐2‐yl)pyridines, 3 and 10 , utilizing the readily available amide 7 is described. Incorporation of the 3‐ t ‐butylamino‐2‐hydroxypropoxy side chain onto 3 provided 2 , a potential bioisostere of 1 . The antihypertensive activities of 2 and 12 were evaluated in the spontaneously hypertensive rat model.
Visualizing massive multi-digraphs (2002)

We describe MGV, an integrated visualization and exploration system for massive multi-digraph navigation. MGV's only assumption is that the vertex set of the underlying digraph corresponds to the set of leaves of a predetermined tree T. MGV builds an out-of-core graph hierarchy and provides mechanisms to plug in arbitrary visual representations for each graph hierarchy slice. Navigation from one level to another of the hierarchy corresponds to the implementation of a drill-down interface. In order to provide the user with navigation control and interactive response, MGV incorporates a number of visualization techniques like interactive pixel-oriented 2D and 3D maps, statistical displays, multi-linked views, and a zoomable label based interface. This makes the association of geographic information and graph data very natural. MGV follows the client-server paradigm and it is implemented in C and Java-3D. We highlight the main algorithmic and visualization techniques behind the tools and point out along the way several possible application scenarios. Our techniques are being applied to multi-graphs defined on vertex sets with sizes ranging from 100 million to 250 million vertices.
Requirement for p53 and p21 to Sustain G <sub>2</sub> Arrest After DNA Damage (1998)

After DNA damage, many cells appear to enter a sustained arrest in the G2 phase of the cell cycle. It is shown here that this arrest could be sustained only when p53 was present in the cell and capable of transcriptionally activating the cyclin-dependent kinase inhibitor p21. After disruption of either the p53 or the p21 gene, gamma radiated cells progressed into mitosis and exhibited a G2 DNA content only because of a failure of cytokinesis. Thus, p53 and p21 appear to be essential for maintaining the G2 checkpoint in human cells.
Identification of a B cell-dependent subpopulation of multiple sclerosis by measurements of brain-reactive B cells in the blood (2014)

B cells are increasingly coming into play in the pathogenesis of multiple sclerosis (MS). Here, we screened peripheral blood mononuclear cells (PBMC) from patients with clinically isolated syndrome (CIS), MS, other non-inflammatory neurological, inflammatory neurological or autoimmune diseases, and healthy donors for their B cell reactivity to CNS antigen using the enzyme-linked immunospot technique (ELISPOT) after 96 h of polyclonal stimulation. Our data show that nine of 15 patients with CIS (60.0%) and 53 of 67 patients with definite MS (79.1%) displayed CNS-reactive B cells, compared to none of the control donors. The presence of CNS-reactive B cells in the blood of the majority of patients with MS or at risk to develop MS along with their absence in control subjects suggests that they might be indicative of a B cell-dependent subpopulation of the disease.
32,000‐Dalton Subunit of the 1,4‐Dihydropyridine Receptor<sup>a</sup> (1989)

Polyclonal antibodies to the 32,000-Da polypeptide of the 1,4-dihydropyridine receptor of the voltage-dependent Ca2+ channel have been produced and used to characterize the association of the 32,000-Da polypeptide (gamma subunit) with other subunits of the dihydropyridine receptor. The 32,000-Da polypeptide was found to copurify with alpha 1 and alpha 2 subunits at each step of the purification of the dihydropyridine receptor. Monoclonal antibodies against the alpha 1 and beta subunits immunoprecipitate the digitonin-solubilized dihydropyridine receptor as a multisubunit complex that includes the 32,000-Da polypeptide. Polyclonal antibodies generated against both the nonreduced and reduced forms of the alpha 2 subunit and the gamma subunit have been used to show that the 32,000-Da polypeptide is not a proteolytic fragment of a larger component of the dihydropyridine receptor and not disulfide linked to the alpha 2 subunit. Our results demonstrate that the 32,000-Da polypeptide (gamma subunit) is an integral and distinct component of the dihydropyridine receptor.
Online flooding prognosis in packed columns by monitoring parameter change in EGARCH model (2017)

In the chemical industry, packed columns are commonly used operating units for separation. However, the flooding phenomenon often reduces the efficiency of packed columns and interferes with the performance of the system. Due to this reason, research on the real-time prognosis of flooding becomes a necessity in practice. Pressure drop is a key factor that indicates flooding phenomenon in packed columns. In this paper, the trajectory of pressure drop in each time window is modeled with an exponential generalized autoregressive conditional heteroskedastic (EGARCH) process. The onset of flooding is then implied by the parameter change of the model. To capture the change in an efficient manner, a nonparametric charting technique is adopted for statistical process control (SPC). The feasibility and efficiency of the proposed method are illustrated by the experimental results.
Standard pulse oximeters can be used to monitor respiratory rate (2003)

Wavelet transforms permit the accurate determination of respiratory rate by a standard pulse oximeter.
In vivo tests of nucleic acid‐based metallo‐β‐lactamase inhibitors in cultures of Bacillus cereus 5/B/6 (2006)

β‐Lactam antibiotics such as penicillins and cephalosporins are the most heavily prescribed antibiotics in clinical use today. The major mechanism by which bacteria become resistant to β‐lactam antibiotics is by production of enzymes called β‐lactamases that catalyze the hydrolytic inactivation of these antibiotics. Previously, we reported the discovery of a 10‐residue single‐stranded DNA (ss‐DNA) that is a potent inhibitor of the B. cereus 5/B/6 metallo‐β‐lactamase [R. W. Shaw and S. ‐K. Kim, FASEB Journal 17 , p. A981 (2003)]. We have developed an in vivo assay of metallo‐β‐lactamase inhibitors of the B. cereus 5/B/6 metallo‐β‐lactamase. Buffered solutions (40 μL) of a combination of cephalexin (antibiotic) plus the ss‐DNA (inhibitor) or antibiotic alone were transferred to 1 cm diameter filter paper disks and the disks were placed on the surface of plates inoculated with the metallo‐β‐lactamase‐producing bacterium B. cereus 5/B/6. The control disks contained 0.02 mM cephalexin dissolved in 50 mM MOPS buffer, pH = 7.0. Disks with the inhibitor contained 7.5 mM ss‐DNA and 0.02 mM cephalexin dissolved in 50 mM MOPS buffer, pH = 7.0. Control disks with just β‐lactam antibiotic alone displayed no inhibition of bacterial cell growth after 8 hours of growth at 30° C. On the same plates, disks that included the ss‐DNA displayed a clear inhibition of growth around those disks. Hence, the combination of the ss‐DNA metallo‐β‐lactamase inhibitor with cephalexin was able to kill B. cereus cells under conditions in which cephalexin alone could not. It is notable that the ss‐DNA was stable enough to cause cell death over an eight‐hour period. Supported by TTU HHMI .
Real-Time Imaging of Cardiac Strain using Ultra-Fast HARP Sequence (2001)

Introduction Tagged MR imaging was introduced in 1988 and has been employed extensively for the non-invasive visualization of cardiac motion and deformation. However, the requirement for patients to breath-hold during the lengthy image acquisition times (8-20 heart beats per slice), and the subsequent laborious post-processing has limited its adoption as a quantitative clinical tool for diagnosis and monitoring. The HARP technique [1] was proposed recently as a novel method for quantifying in-plane motion using MR tagging methodology. Tagged MR images comprise multiple spectral peaks (see Figure 1) in the Fourier domain. HARP exploits the fact that, when one of the offcenter spectral peaks is isolated and inverse Fourier transformed, the phase of the resulting image is directly related to the motion of the underlying tissue. To date, this methodology has been demonstrated and validated as an extremely efficient means for extracting displacement and strain measurements from tagged MR datasets. Here we describe the development of a pulse sequence and postprocessing software specifically optimized for the real-time acquisition, reconstruction and display of HARP images capable of providing full visualization of the in-plane myocardial motion from just 2 cardiac cycles. This very short acquisition time significantly reduces (or eliminates) the burden of breath-holding for the patient. Typically, 12-20 cardiac phases are acquired per R-R cycle with motion sensitivity switching (horizontal/vertical) on alternate heartbeats. The pulse sequence may be run continuously for cardiac monitoring with the acquired HARP datasets being automatically reconstructed and displayed in real-time after each heart-beat.
Convolutional neural network-based inspection of metal additive manufacturing parts (2019)

Purpose Part quality inspection is playing a critical role in the metal additive manufacturing (AM) industry. It produces a part quality analysis report which can be adopted to further improve the overall part quality. However, the part quality inspection process puts heavy reliance on the engineer’s background and experience. This manual process suffers from both low efficiency and potential errors and, therefore, cannot meet the requirement of real-time detection. The purpose of this paper is to look into a deep neural network, Convolutional Neural Network (CNN), towards a robust method for online monitoring of AM parts. Design/methodology/approach The proposed online monitoring method relies on a deep CNN that takes a real metal AM part’s images as inputs and the part quality categories as network outputs. The authors validate the efficacy of the proposed methodology by recognizing the “beautiful-weld” category from material CoCrMo top surface images. The images of “beautiful-weld” parts that show even hatch lines and appropriate overlaps indicate a good quality of an AM part. Findings The classification accuracy of the developed method using limited information of a small local block of an image is 82 per cent. The classification accuracy using the full image and the ensemble of model outputs is 100 per cent. Originality/value A real-world data set of high resolution images of ASTM F75 I CoCrMo-based three-dimensional printed parts (Top surface images with magnification 63×) annotated with categories labels. Development of a CNN-based classification model for the supervised learning task of recognizing a “beautiful-weld” AM parts. The classification accuracy using the full image and the ensemble of model outputs is 100 per cent.
Dynamically Reconfigurable FPGA-Based Multiprocessing and Fault Tolerance. (1996)

Processor replication is a straightforward yet general method for contending with a range of failure modes in computing systems. Architectural support is required if faults in the processors or their software are to be tolerated efficiently in the field. Until now, hardware-intensive solutions have not been seriously considered because dedicating resources solely to fault tolerance lowers utilization--especially at times when fault tolerance is not required. Alternately, software-intensive solutions, although flexible, require coping with slower speeds. Together these factors culminate in designs that are less than optimum. Our objective in this research is to eliminate these problems and limitations by adding a multiprocessing capability so that the redundant hardware is used selectively. We propose a novel architecture we refer to as Dynamic Reconfigurability Assisting Fault Tolerance (DRAFT) that has multiprocessing (MP) and fault-tolerant (FT) modes. Our architecture is flexible in that processors do not have to be tightly synchronized, and it permits unconstrained combinations of FT and MP applications to execute concurrently for efficient processor utilization. We capitalize on dynamically reconfigurable Field-Programmable Gate Array (FPGA) technology, where portions of the logic can be changed without disturbing the rest of the array. We demonstrate our tools and techniques for reconfiguring the FPGA, even while it operates, to create a virtual FPGA is that is much larger than the physical FPGA. By embedding FT and MP support functions in the virtual FPGA, we avoid a significant reliability penalty and simultaneously accelerate application throughput. We have analyzed the proposed architecture and evaluated it with respect to performance, cost, scalability, reliability, and configurability. Based on all of these criteria, we have shown that our approach is superior to comparable designs. Compared to a dedicated processor, DRAFT roughly doubles application throughput while halving the failure rate.
Constitutive or seed‐specific overexpression of <scp>A</scp>rabidopsis <i><scp>G</scp>‐protein γ subunit 3</i> (<i><scp>AGG</scp>3</i>) results in increased seed and oil production and improved stress tolerance in <i><scp>C</scp>amelina sativa</i> (2013)

Heterotrimeric G-proteins consisting of Gα, Gβ and Gγ subunits play an integral role in mediating multiple signalling pathways in plants. A novel, recently identified plant-specific Gγ protein, AGG3, has been proposed to be an important regulator of organ size and mediator of stress responses in Arabidopsis, whereas its potential homologs in rice are major quantitative trait loci for seed size and panicle branching. To evaluate the role of AGG3 towards seed and oil yield improvement, the gene was overexpressed in Camelina sativa, an oilseed crop of the Brassicaceae family. Analysis of multiple homozygous T4 transgenic Camelina lines showed that constitutive overexpression of AGG3 resulted in faster vegetative as well as reproductive growth accompanied by an increase in photosynthetic efficiency. Moreover, when expressed constitutively or specifically in seed tissue, AGG3 was found to increase seed size, seed mass and seed number per plant by 15%-40%, effectively resulting in significantly higher oil yield per plant. AGG3 overexpressing Camelina plants also exhibited improved stress tolerance. These observations draw a strong link between the roles of AGG3 in regulating two critical yield parameters, seed traits and plant stress responses, and reveal an effective biotechnological tool to dramatically increase yield in agricultural crops.
Valley-Coupled-Spintronic Non-Volatile Memories With Compute-In-Memory Support (2020)

In this work, we propose valley-coupled spin-hall memories based on monolayer WSe2. The key features of the proposed memories are (a) the ability to switch magnets with perpendicular magnetic anisotropy and (b) an integrated gate that can modulate the charge/spin current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> ) flow. The former attribute results in high energy efficiency (compared to the Giant-Spin Hall (GSH) effect-based devices with in-plane magnetic anisotropy magnets). The latter feature leads to a compact accesstransistor-less memory array design. We experimentally measure the gate controllability of the current as well as the non-local resistance associated with valley-coupled spin-hall effect. Based on the measured data, we develop a simulation framework to propose and analyze single-ended and differential valley-coupled spin-hall effect based magnetic memories (VSH-MRAM and DVSH-MRAM, respectively). At the array level, the proposed VSH/DVSH-MRAMs achieve 50%/11% lower write time, 59%/67% lower write energy, 12%/30% lower read time and 35%/41% lower read energy at iso-sense margin, compared to single-ended/differential Giant-Spin Hall (GSH/DGSH)-MRAMs. System level evaluation in the context of general-purpose processor and intermittently-powered system shows up to 3.14X and 1.98X better energy efficiency for the proposed (D)VSH-MRAMs over (D)GSH-MRAMs respectively. Further, the differential sensing of the proposed DVSH-MRAM leads to natural and simultaneous in-memory computation of bit-wise AND and NOR logic functions. Using this feature, we design a computation-in-memory (CiM) architecture that performs Boolean logic and addition with a single array access. System analysis performed by integrating our DVSH-MRAM: CiM in the Nios II processor shows up to 2.57X total energy savings, compared to DGSH-MRAM: CiM.
On-chip whispering-gallery-mode lasers for sensing applications (2012)

Whispering-Gallery-Mode (WGM) microresonators have shown great promise for ultra-sensitive and label-free chemical and biological sensing. The linewidth of a resonant mode determines the smallest resolvable changes in the WGM spectrum, which, in turn, affects the detection limit. The fundamental limit is set by the linewidth of the resonant mode due to material absorption induced photon loss. We report a real-time detection method with single nanoparticle resolution that surpasses the detection limit of most passive micro/nano photonic resonant devices. This is achieved by using an on-chip WGM microcavity laser as the sensing element, whose linewidth is much narrower than its passive counterpart due to optical gain in the resonant lasing mode. In this microlaser based sensing platform, the first binding nanoparticle induces splitting of the lasing line, and the subsequent particles alter the amount of splitting, which can be monitored by measuring the beat frequency of the split modes. We demonstrate detection of polystyrene and gold nanoparticles as small as 15 nm and 10 nm in radius, respectively, and Influenza A virions. The built-in self-heterodyne interferometric method achieved in the monolithic microlaser provides a self-referencing scheme with extraordinary sensitivity, and paves the way for detection and spectroscopy of nano-scale objects using micro/nano lasers.
Optical Multidimensional Coherent Spectroscopy (2023)

Abstract Optical multidimensional coherent spectroscopy provides information about the structure and excitation dynamics in a broad range of material systems. This book focuses on systems of interest in physics, including atomic vapors, semiconductor nanostructures and two-dimensional materials. An introduction to ultrafast spectroscopy and the fundamental concepts of multidimensional coherent spectroscopy applies to all material systems. Relevant experimental implementations, including phase-stabilized crossed-beams, frequency-tagged fully-collinear, three-dimensional and frequency-comb based methods. The use of the method to study atomic vapors, semiconductor quantum wells, semiconductor quantum dots and two-dimensional materials are described in separate chapters. The final chapters survey the use of the method in some other areas and speculate on future directions.
A Simple Chiral Synthesis of the Taxol Side Chain (1992)

We report a highly diastereoselective synthesis of (3R,4S)-3-hydroxy-4-phenyl-2-azetidinone (11) using L-threonine as a chiral template. This compound has been utilized in the partial synthesis of taxol from 10-desacetyl baccatin III (2a).
Pyridinedicarboxylates, the first mechanism-derived inhibitors for prolyl 4-hydroxylase, selectively suppress cellular hydroxyprolyl biosynthesis. Decrease in interstitial collagen and Clq secretion in cell culture (1987)

Two pyridinedicarboxylates, predicted [Hanauske-Abel (1983) M.D.-Ph.D. Thesis, Philipps Universität Marburg] and later found to be potent reversible inhibitors of purified prolyl 4-hydroxylase [Majaama, Hanauske-Abel, Günzler & Kivirikko (1984) Eur. J. Biochem. 138, 239-245] were investigated with respect to their effect on hydroxyprolyl biosynthesis in the fibroblast/collagen and the macrophage/Clq systems, and the effect was compared with that of the iron chelator 2,2'-dipyridyl, the compound usually employed to inhibit cellular hydroxyprolyl formation. Only the enzyme-mechanism-derived pyridinedicarboxylates were highly selective inhibitors, and only they lacked overt cytotoxicity. Morphologically, their effect was restricted to the site of cellular hydroxyprolyl biosynthesis, i.e. the cisternae of the rough-surfaced endoplasmic reticulum. They were equally effective in the different cell types studied, and human and guinea-pig fibroblasts showed the same sensitivity. The minimal lipophilicity of the pyridinedicarboxylates necessitated high concentrations to achieve suppression of cellular hydroxyprolyl formation, but lipophilic bio-activatable pro-inhibitors may overcome this disadvantage. For the first time, experimental evidence is presented suggesting that, in cell culture, the biosynthesis of interstitial collagens and Clq can be suppressed selectively, identifying the pyridinedicarboxylates as promising pilot compounds for experiments in vivo.