gebhart/patrepeval huggingface dataset:
Gelation And Mechanical Response of Patchy Rods (2016)

We perform Brownian dynamics simulations to study the gelation of suspensions of attractive, rod-like particles. We show that in detail the rod–rod surface interactions can dramatically affect the dynamics of gelation and the structure and mechanics of the networks that form. If the attraction between the rods is perfectly smooth along their length, they will collapse into compact bundles. If the attraction is sufficiently corrugated or patchy, over time, a rigid space-spanning network will form. We study the structure and mechanical properties of the networks that form as a function of the fraction of the surface, f, that is allowed to bind. Surprisingly, the structural and mechanical properties are non-monotonic in f. At low f, there are not a sufficient number of cross-linking sites to form networks. At high f, rods bundle and form disconnected clusters. At intermediate f, robust networks form. The elastic modulus and yield stress are both non-monotonic in the surface coverage. The stiffest and strongest networks show an essentially homogeneous deformation under strain with rods re-orienting along the extensional axis. Weaker, more clumpy networks at high f re-orient relatively little with strong non-affine deformation. These results suggest design strategies for tailoring surface interactions between rods to yield rigid networks with optimal mechanical properties.
Quantification of the Mesoscale Spatiotemporal Heterogeneities in Nickel-Rich Layered Oxide Cathodes By Raman Spectroscopy (2022)

Lithium-ion batteries consisting of the particulate porous electrodes, are the dominant energy storage devices, however, they suffer from random failures and safety-related accidents. Such arbitrary incidents arise from the spatiotemporal heterogeneities occurring due to the material thermodynamics [1] which results to local hot and cold spots and early battery failures. The past investigations of the heterogeneities in the battery materials rely on the sophisticated synchrotron X-ray methods [2]–[4] , which are not easily accessible. Instead, in this study, we employ Raman spectroscopy on an in situ benchtop setup which provides several advantages while investigating the true electrochemical kinetics in graphite electrodes, such as: (i) the setup houses practical porous NMC532 cathodes under realistic electrochemical surroundings; (ii) the high resolution of 1-2 µm provides sufficient information on the larger cathode particles; (iii) the method can analyze hundreds of particles, statistically representing the entire composite electrode; and (iv) the spectra can be quantified to reveal the actual reaction area, thus revealing high-fidelity real-time electrochemical performance. We use this simple but precision method to track and analyze the active reaction regions at the mesoscale in the NMC532 electrode to obtain the true local current density, which was found to be an order of magnitude higher than the globally-averaged current density adopted by the existing studies. Raman spectroscopy can distinguish the vibrational modes of NMC532 with varying Li ion concentration. Since NMC532 is a solid-solution material, the Raman spectrum at each selected location can be deconvoluted into three distinct phases: empty, completely lithiated and partially lithiated. The partially lithiated regions participate in the surface reaction and can be identified to reveal the active reaction area. Thus, we quantified the active area fraction under slow galvanostatic conditions and generated a map of active regions with varying global Li ion fractions. Our results show that only 18% – 50% of the total particle area is active at any instant leading to higher local current densities than the globally-averaged electrode responses. The methods developed in this study are critical to estimate the kinetic parameters using true electrochemical responses and further aid in the design of the particulate porous electrodes. References [1] S. Agrawal, P. Bai, Cell Reports Phys. Sci. 2022 , 3 , 1. [2] S.J. Harris, A. Timmons, D.R. Baker, C. Monroe, Chem. Phys. Lett. 2010 , 485 , 265. [3] C. Tian, Y. Xu, D. Nordlund, F. Lin, J. Liu, Z. Sun, Y. Liu, M. Doeff, Joule 2018 , 2 , 464. [4] S. Fang, M. Yan, R.J. Hamers, J. Power Sources 2017 , 352 , 18.
Recall of preexisting cross-reactive B cell memory after Omicron BA.1 breakthrough infection (2022)

Understanding immune responses after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection will facilitate the development of next-generation vaccines. Here, we profiled spike (S)-specific B cell responses after Omicron/BA.1 infection in messenger RNA-vaccinated donors. The acute antibody response was characterized by high levels of somatic hypermutation and a bias toward recognition of ancestral SARS-CoV-2 strains, suggesting the early activation of vaccine-induced memory B cells. BA.1 breakthrough infection induced a shift in B cell immunodominance hierarchy from the S2 subunit, which is highly conserved across SARS-CoV-2 variants of concern (VOCs), and toward the antigenically variable receptor binding domain (RBD). A large proportion of RBD-directed neutralizing antibodies isolated from BA.1 breakthrough infection donors displayed convergent sequence features and broadly recognized SARS-CoV-2 VOCs. Together, these findings provide insights into the role of preexisting immunity in shaping the B cell response to heterologous SARS-CoV-2 variant exposure.
Through-pellicle inspection using EUV ptychography microscope (Conference Presentation) (2019)

Extreme ultraviolet (EUV) lithography is going to be inserted into high volume manufacturing (HVM) of 7 nm technology node device. However, the insertion of EUV pellicle is still a major issue. Since particles on the pellicle larger than a critical size can act as killing defects on the final wafer pattern, through-pellicle inspection has to be preceded before applying into the lithography process. Even though non-actinic techniques which use deep ultraviolet (DUV) or e-beam light source can be used for preliminary inspection, actinic technique is still indispensable for the precise aerial image review and defect detection. In this study, through-pellicle inspection was performed by using EUV scanning lensless imaging (ESLI), which has been developed as an actinic inspection technique. ESLI uses a coherent light source generated by high-order harmonic generation (HHG) and coherent diffraction imaging (CDI) method which reconstructs the object image using the diffracted light from EUV mask. We especially adopted ptychography for large area through-pellicle inspection. Ptychography, multi-shot CDI which uses a series of diffraction patterns with redundancy, enables more accurate object reconstruction compared to conventional CDI method. We imaged EUV mask which has 128 nm half-pitch (HP) line and space (L/S) patterns. Also, mask inspection performance of ESLI was verified by comparing the reconstructed imaging results with CD-SEM image results. We also assessed defect detectability of ESLI by defect mapping of pellicle with various size defect. Furthermore, through-pellicle EUV mask imaging was executed for the study about acceptable defect size on EUV pellicle. In conclusion, we confirmed the ESLI’s feasibility for EUV pellicle qualification and defect inspection.
Decontamination Strategy for Large Area and/or Equipment Contaminated with Chemical and Biological Agents using a High Energy Arc Lamp (HEAL) (2009)

A strategy for the decontamination of large areas and or equipment contaminated with Biological Warfare Agents (BWAs) and Chemical Warfare Agents (CWAs) was demonstrated using a High Energy Arc Lamp (HEAL) photolysis system. This strategy offers an alternative that is potentially quicker, less hazardous, generates far less waste, and is easier to deploy than those currently fielded by the Department of Defense (DoD). For example, for large frame aircraft the United States Air Force still relies on the combination of weathering (stand alone in environment), air washing (fly aircraft) and finally washing the aircraft with Hot Soapy Water (HSW) in an attempt to remove any remaining contamination. This method is laborious, time consuming (upwards of 12+ hours not including decontamination site preparation), and requires large amounts of water (e.g., 1,600+ gallons for a single large frame aircraft), and generates large amounts of hazardous waste requiring disposal. The efficacy of the HEAL system was demonstrated using diisopropyl methyl phosphonate (DIMP) a G series CWA simulant, and Bacillus globigii (BG) a simulant of Bacillus anthracis. Experiments were designed to simulate the energy flux of a field deployable lamp system that could stand-off 17 meters from a 12m2 target area and uniformly expose a surface at 1360 W/m2. The HEAL system in the absence of a catalyst reduced the amount of B. globigii by five orders of magnitude at a starting concentration of 1.63 x 107 spores. In the case of CWA simulants, the HEAL system in the presence of the catalyst TiO2 effectively degraded DIMP sprayed onto a 100mm diameter Petri dish in 5 minutes.
Basic Introduction to Bioelectromagnetics (2018)

Basic Introduction to Bioelectromagnetics, Third Edition, is a primary source for medical technologists and life scientists seeking to understand how electromagnetic fields interact with the body, and how they are used in medical applications. Instead of the complex math commonly used when analyzing electromagnetics, this book uses graphical methods and simple equations. The third edition is updated with color graphics that show the fields in bright, clear colors. Each concept is presented with an associated discussion and application, including MRI, NMR, hyperthermia, neural stimulation, ultrasound, and cardiac pacing/defibrillation. Offering a simplified explanation of a very complex subject, this third edition provides an accessible introduction for life scientists and medical technologist on how EM fields work, what controls them, and the factors important to experimental setups and medical applications. This qualitative and illustrative book: Covers the entire frequency spectrum from direct current (DC) up through optical frequencies. Includes more than 200 illustrations, 65 in color, and 40 medical applications. Incorporates examples from real-world applications to explain concepts. Concentrates on the qualitative explanation of the key concepts, fundamental principles, and characteristic behaviors of EM fields, without complicated mathematics. Offers practical rules of thumb to understand real situations. Requires only a background in algebra, in contrast to typical EM books that require vector calculus and differential equations.
Technology to Facilitate the Use of Impaired Waters in Cooling Towers (2012)

The project goal was to develop an effective silica removal technology and couple that with existing electro-dialysis reversal (EDR) technology to achieve a cost effective treatment for impaired waters to allow for their use in the cooling towers of coal fired power plants. A quantitative target of the program was a 50% reduction in the fresh water withdrawal at a levelized cost of water of $3.90/Kgal. Over the course of the program, a new molybdenum-modified alumina was developed that significantly outperforms existing alumina materials in silica removal both kinetically and thermodynamically. The Langmuir capacity is 0.11g silica/g adsorbent. Moreover, a low cost recycle/regeneration process was discovered to allow for multiple recycles with minimal loss in activity. On the lab scale, five runs were carried out with no drop in performance between the second and fifth run in ability to absorb the silica from water. The Mo-modified alumina was successfully prepared on a multiple kilogram scale and a bench scale model column was used to remove 100 ppm of silica from 400 liters of simulated impaired water. Significant water savings would result from such a process and the regeneration process could be further optimized to reduce water requirements. Current barriers to implementation are the base cost of the adsorbent material and the fine powder form that would lead to back pressure on a large column. If mesoporous materials become more commonly used in other areas and the price drops from volume and process improvements, then our material would also lower in price because the amount of molybdenum needed is low and no additional processing is required. There may well be engineering solutions to the fine powder issue; in a simple concept experiment, we were able to pelletize our material with Boehmite, but lost performance due to a dramatic decrease in surface area.
Achievable DoF Regions of MIMO Networks with Imperfect CSIT (2016)

We focus on a two-receiver Multiple-Input-Multiple-Output (MIMO) Broadcast Channel (BC) and Interference Channel (IC) with an arbitrary number of antennas at each node. We assume an imperfect knowledge of local Channel State Information at the Transmitters (CSIT), whose error decays with the Signal-to-Noise-Ratio. With such configuration, we characterize the achievable Degrees-of-Freedom (DoF) regions in both BC and IC, by proposing a Rate-Splitting approach, which divides each receiver's message into a common part and a private part. Compared to the RS scheme designed for the symmetric MIMO case, this scheme is suitable for the general asymmetric deployment with an arbitrary number of antennas at each node. In BC, the proposed block 1) employs an unequal power allocation to the private messages of the two receivers, 2) exploits the benefit of having an extra spatial dimension at one receiver, and 3) is carried out with a Space-Time transmission. These features enable the scheme to yield a greater DoF region than trivially extending the scheme designed for the symmetric case. In IC, we modify the scheme proposed for the BC case by applying a linear transformation to the channel matrices. Such a linear transformation allows us to identify the signal space where the two transmitted signals interfere with each other and propose a proper power allocation policy. The achievable DoF regions are shown to be optimal for some antenna configurations.
Silica-supported iron oxide nanoparticles: unexpected catalytic activity in hydrogenation of phenylacetylene (2017)

Hydrogenation of phenylacetylene in liquid phase (100–150 °C, 6–20 bar H2) over FeOx / SiO2 catalysts prepared by thermal decomposition of ammonium trioxalatoferrate affords styrene with selectivities 70–80% depending on temperature and pressure.
Neurologic Recovery Associated with Anterior Decompression of Spine Fractures at the Thoracolumbar Junction (T12–L1) (1992)

Between 1981 and 1990, twenty-two patients with incomplete neurologic deficits after thoracolumbar junction fractures were treated by anterior decompression and stabilization. Two patients were unavailable for follow-up examination, eleven underwent spinal canal decompression within 48 hours of injury (Group A); and nine patients underwent surgical decompression in an average of 61 days after injury (Group B). Neurologic recovery was analyzed by a modified Frankel grading system, the ASIA motor point scale and conus medullaris function. Patients were followed for an average of 3.5 years (range, 6-92 months). No patients had any deterioration in neurologic function after surgery. Patients in Group A had a modified Frankel grade improvement with a median of two grades and a mean American Spine Injury Association motor point improvement of 21.1 +/- 4.1. Four of nine patients with conus medullaris deficits demonstrated complete functional bladder and bowel return postoperatively. Those patients in Group B had a modified Frankel grade improvement with a median of one grade and a mean ASIA motor point improvement of 7.6 +/- 1.7. None of the six patients with conus medullaris injuries showed complete improvement in bladder or bowel function postoperatively. The modified Frankel grade and ASIA motor point score improvements were significant when the two groups were compared (P less than 0.04 and P less than 0.01, respectively). In this series of patients, early anterior decompression for traumatic injuries at the thoracolumbar junction was associated with improved rates of neurologic recovery when compared to late decompression.
Setting Rules for Post-ablation and Follow-Up (2012)

Focal therapy has emerged as a less aggressive treatment alternative for a highly select group of men with early stage prostate cancer. Despite advances in ablative technology and imaging, focal therapy is still considered to be experimental or investigative by most centers. In addition, focal therapy has been broadly defined including a wide range of treatment modalities and templates. As a result of these issues, no standardized criteria or consensus protocols have been adopted for post-ablation oncological and functional follow-up and surveillance. In an effort to move closer to the adoption of a more unified approach, we review the relevant literature and suggest guidelines for post-ablation biopsies, use of PSA data, imaging, patient functional evaluation, and reporting of side effects.
QS5: The Effect of Stem Cells and Local Tacrolimus on Neurite Extension (2021)

Purpose: Application of mesenchymal stem cells (MSCs) or tacrolimus (FK506), an FDA approved immunosuppressant, to nerve grafts has been a topic of interest to enhance peripheral nerve regeneration. The aim of this study was to investigate the combined effect of MSCs and local delivery of FK506 on nerve regeneration when applied to nerve autografts and decellularized nerve allografts. Methods: A three-dimensional (3D) in vitro compartmented cell culture system, validated by Tajdaran et al (2019), consisted of rat neonatal dorsal root ganglion (DRG) adjacent to rat nerve autograft or decellularized allograft. This model was used to evaluate regenerating neurites from the DRG into the peripheral nerve scaffold. Nerve autografts and decellularized allografts were augmented with (i) dynamic undifferentiated MSC seeding, (ii) local application of FK506 (100 ng/mL) or (iii) both (N=9/group). Local application was ensured by isolating the central system (i.e. DRG side) from the peripheral system (i.e. nerve graft side), where treatment was applied. After 48-hours of incubation, DRG-nerve graft constructs were collected, fixed, sectioned and stained against neurofilament-160 to measure neurite extension. CD90 staining was used to confirm stem cell characterization. Results: All grafts treated with MSCs confirmed CD90 expression. Compared to untreated autografts, neurite extension in autografts treated with FK506 and autografts treated with MSCs and FK506 combined were found superior (P&lt;0.001 and P=0.0001, respectively), and comparable to autografts treated with MSCs (P=0.12). Compared to untreated allografts, allografts treated with FK506, and allografts treated with MSCs and FK506 were found superior (P&lt;0.001 and P=0.0001, respectively), and allografts treated with MSCs were found comparable (P=0.09). All autograft groups were found superior compared to their respective allograft treatment group (P&lt;0.05). Solely allografts receiving combined treatment were found superior to untreated autografts (P&lt;0.05). Conclusion: MSCs or FK506 treatment improved neurite outgrowth and when combined, this resulted in significant synergistic neurite extension in both autografts and allografts in comparable patterns. Schematic overview of 3D compartmented cell culture system for isolated evaluation of treatment with MSCs and local FK506 in vitro. A 3.5 mm autograft or allograft with or without undifferentiated MSC seeding is attached to a DRG. DRG-nerve graft constructs are placed through a silicone isolator in the middle of a 24-wells plate to isolate the DRG from the nerve graft. FK506 containing media was added to the nerve graft side.
Fixed pattern noise column drift compensation (CDC) for digital moving picture cameras (2010)

In CMOS image sensors tiny semiconductor variations cause a distortion of the image known as fixed pattern noise (FPN). With a good FPN compensation CMOS sensors can deliver very good image quality. Compensation algorithms differ in complexity, maximum frame rate, and compensation quality with thermal drift. This paper analyzes existing approaches to offset FPN compensation and their drawbacks. We also show a new compensation algorithm that offers fine grained per-pixel compensation and is able to compensate temperature variations while still operating at the maximum sensor frame rate. This enables the construction of motion picture cameras without active cooling or even temperature measurements while still delivering a high image quality at high frame rates.
Butyrate analogue, isobutyramide, inhibits tumor growth and time to androgen-independent progression in the human prostate LNCaP tumor model (1998)

Progression to androgen independence remains the main obstacle to improving survival and quality of life in patients with advanced prostate cancer. Induction of differentiation may serve as a rational basis for prevention of progression to androgen independence by modulating gene expression activated by castration or upregulated during androgen-independent progression. The objectives of this study were to characterize the in vitro effects of sodium butyrate on human prostate cancer cell growth, PSA gene expression, and differentiation in the LNCaP tumor model and to determine whether tumor progression in vivo is delayed by isobutyramide, an orally bioavailable butyrate analogue with a longer half-life. The effects of isobutyramide on LNCaP tumor growth and serum PSA levels in both intact and castrate male mice were compared to controls. At concentrations >1 mM, butyrate induced dose-dependent changes towards a more differentiated phenotype, G1 cell cycle arrest, and an 80% decrease in LNCaP cell growth rates. PSA gene expression was increased threefold by butyrate, indicative of differentiation-enhanced gene expression. The half-life of isobutyramide in athymic mice was determined by gas chromatography to be 4 h. During a 4 week period in intact-placebo mice, tumor volume and serum PSA increased 4.1- and 6.6-fold, respectively, compared to twofold and 2.7-fold increases in tumor volume and serum PSA in intact-treated mice. During a 7 week period in castrate-placebo mice, tumor volume and serum PSA levels increased 2.4-fold and fourfold, respectively, compared to a 50% reduction in tumor volume and a twofold increase in serum PSA above nadir levels in castrate mice treated with adjuvant isobutyramide. Isobutyramide treatment induced pronounced morphological changes in LNCaP tumor cells, with loss of defined nucleoli and dispersion of chromatin distribution. LNCaP tumor PSA mRNA levels actually increased threefold, indicative of differentiation-enhanced gene expression. This study demonstrates that butyrate causes LNCaP cell cycle arrest and increased PSA gene expression, both indicative of differentiation. The combination of castration and adjuvant isobutyramide was synergistic in delaying tumor progression. Decreased tumor cell proliferation and increased PSA gene expression induced by isobutyramide results in disconcordant changes in serum PSA and tumor volume and reduces the utility of serum PSA as a marker of response to therapy.