gebhart/patrepeval huggingface dataset:
13-fold resolution gain through turbid layer via translated unknown speckle illumination (2017)

Fluorescence imaging through a turbid layer holds great promise for various biophotonics applications. Conventional wavefront shaping techniques aim to create and scan a focus spot through the turbid layer. Finding the correct input wavefront without direct access to the target plane remains a critical challenge. In this paper, we explore a new strategy for imaging through turbid layer with a large field of view. In our setup, a fluorescence sample is sandwiched between two turbid layers. Instead of generating one focus spot via wavefront shaping, we use an unshaped beam to illuminate the turbid layer and generate an unknown speckle pattern at the target plane over a wide field of view. By tilting the input wavefront, we raster scan the unknown speckle pattern via the memory effect and capture the corresponding low-resolution fluorescence images through the turbid layer. Different from the wavefront-shaping-based single-spot scanning, the proposed approach employs many spots (i.e., speckles) in parallel for extending the field of view. Based on all captured images, we jointly recover the fluorescence object, the unknown optical transfer function of the turbid layer, the translated step size, and the unknown speckle pattern. Without direct access to the object plane or knowledge of the turbid layer, we demonstrate a 13-fold resolution gain through the turbid layer using the reported strategy. We also demonstrate the use of this technique to improve the resolution of a low numerical aperture objective lens allowing to obtain both large field of view and high resolution at the same time. The reported method provides insight for developing new fluorescence imaging platforms and may find applications in deep-tissue imaging.
A New Class of Uranium Oxide Based Catalysts for the Oxidative Destruction of Benzene and Butane Volatile Organic Compounds (1996)

The oxidative destruction of two typical volatile organic compounds (VOCs), benzene and butane, have been investigated by uranium oxide based catalysts. A new range silica supported uranium oxide catalysts have also been synthesised and tested under industrially relevant conditions.. Catalytic activity studies have shown that U3O8 is an active catalyst for the destruction of both compounds at high gas hourly space velocity. Comparison with Co3O4, a known active combustion catalyst, showed that U3O8 was more active under the majority of our experimental conditions. The silica supported catalysts also showed high activity for benzene and butane destruction.. Doping the supported catalyst with chromium considerably enhanced the activity for butane destruction. These studies have demonstrated that under commercially realistic operating conditions, catalysts based on uranium oxide show high activity for the oxidative destruction of benzene and butane, which are considered to be representative of two types of very different common volatile organic compounds.
Data from Reducing <i>Ex Vivo</i> Culture Improves the Antileukemic Activity of Chimeric Antigen Receptor (CAR) T Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;The success of chimeric antigen receptor (CAR)–mediated immunotherapy in acute lymphoblastic leukemia (ALL) highlights the potential of T-cell therapies with directed cytotoxicity against specific tumor antigens. The efficacy of CAR T-cell therapy depends on the engraftment and persistence of T cells following adoptive transfer. Most protocols for T-cell engineering routinely expand T cells &lt;i&gt;ex vivo&lt;/i&gt; for 9 to 14 days. Because the potential for engraftment and persistence is related to the state of T-cell differentiation, we hypothesized that reducing the duration of &lt;i&gt;ex vivo&lt;/i&gt; culture would limit differentiation and enhance the efficacy of CAR T-cell therapy. We demonstrated that T cells with a CAR-targeting CD19 (CART19) exhibited less differentiation and enhanced effector function &lt;i&gt;in vitro&lt;/i&gt; when harvested from cultures at earlier (day 3 or 5) compared with later (day 9) timepoints. We then compared the therapeutic potential of early versus late harvested CART19 in a murine xenograft model of ALL and showed that the antileukemic activity inversely correlated with &lt;i&gt;ex vivo&lt;/i&gt; culture time: day 3 harvested cells showed robust tumor control despite using a 6-fold lower dose of CART19, whereas day 9 cells failed to control leukemia at limited cell doses. We also demonstrated the feasibility of an abbreviated culture in a large-scale current good manufacturing practice–compliant process. Limiting the interval between T-cell isolation and CAR treatment is critical for patients with rapidly progressing disease. Generating CAR T cells in less time also improves potency, which is central to the effectiveness of these therapies. &lt;i&gt;Cancer Immunol Res; 6(9); 1100–9. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Cased Pipe Risk Assessment and Inspection Technologies for Natural Gas Pipelines Operated by Local Distribution Companies (2009)

Abstract Risk based methods to assess a group of cased pipe sections in terms of the corrosion threat are presented, and the development of a tool to evaluate the condition of an individual cased pipe section that might require assessment is described.
ChemInform Abstract: Structure and Mechanism in Cinchona Alkaloid Chemistry: Overturning a 50‐Year‐Old Misconception (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
P‐138: Plasma Beam Alignment of Lyotropic Chromonic Liquid Crystals (2011)

Abstract We have successfully extended the plasma beam alignment technique to the class of lyotropic chromonic liquid crystals (LCLCs). High quality alignment of these materials was obtained in sandwich cells and in dried films coated on a solid substrate. The plasma beam alignment of LCLCs facilitates practical applications of these materials.
Manufacturable 32-Channel Cochlear Electrode Array and Preliminary Assessment of Its Feasibility for Clinical Use (2021)

(1) Background: In this study, we introduce a manufacturable 32-channel cochlear electrode array. In contrast to conventional cochlear electrode arrays manufactured by manual processes that consist of electrode-wire welding, the placement of each electrode, and silicone molding over wired structures, the proposed cochlear electrode array is manufactured by semi-automated laser micro-structuring and a mass-produced layer-by-layer silicone deposition scheme similar to the semiconductor fabrication process. (2) Methods: The proposed 32-channel electrode array has 32 electrode contacts with a length of 24 mm and 0.75 mm spacing between contacts. The width of the electrode array is 0.45 mm at its apex and 0.8 mm at its base, and it has a three-layered arrangement consisting of a 32-channel electrode layer and two 16-lead wire layers. To assess its feasibility, we conducted an electrochemical evaluation, stiffness measurements, and insertion force measurements. (3) Results: The electrochemical impedance and charge storage capacity are 3.11 ± 0.89 kOhm at 1 kHz and 5.09 mC/cm2, respectively. The V/H ratio, which indicates how large the vertical stiffness is compared to the horizontal stiffness, is 1.26. The insertion force is 17.4 mN at 8 mm from the round window, and the maximum extraction force is 61.4 mN. (4) Conclusions: The results of the preliminary feasibility assessment of the proposed 32-channel cochlear electrode array are presented. After further assessments are performed, a 32-channel cochlear implant system consisting of the proposed 32-channel electrode array, 32-channel neural stimulation and recording IC, titanium-based hermetic package, and sound processor with wireless power and signal transmission coil will be completed.
Supplementary Figure S2 from CD44<sup>+</sup> Cells in Head and Neck Squamous Cell Carcinoma Suppress T-Cell–Mediated Immunity by Selective Constitutive and Inducible Expression of PD-L1 (2023)

&lt;p&gt;Supplementary Figure S2. Characterization of CD44- and CD44+ SCCHN cells.&lt;/p&gt;
Notice of Removal: Nonlinear effects in NEMS — Improving frequency stability (2017)

Removed.
Extending Electro-Optic Detection of Short Particle Beams Beyond the Transverse Phonon Resonance (2010)

A technique to noninvasively measure the longitudinal profile of an ultrashort charged particle beam is developed. This technique is based on three‐wave mixing of the particle beam’s self‐fields and an optical probe in a nonlinear material. The resulting mixed field is then diagnosed by a cross‐correlating frequency resolved optical gate, which provides both frequency and phase information about the generated pulse from which, in principle, the temporal profile can be reconstructed. An equation for the generated fields as well as numerical results showing the effects of a chirped probe pulse are presented.
State/Parameter/Disturbance Estimation With an Accelerometer in Precision Motion Control of a Linear Motor (2001)

Abstract In this paper, the use of an accelerometer in precision motion control of linear motors is investigated. The acceleration measurement can provide several advantages. In particular, it can be used with the position measurement for estimation of the position and velocity based on a kinematic model. It can be further utilized for identification of dynamic parameters such as coulomb friction and cogging force as well as for estimation of disturbance. Experimental results verify the effectiveness of the proposed estimation/identification schemes. These schemes are integrated into a two-degree of freedom control system for precision motion control of linear motors. The proposed schemes are evaluated by experiments performed on a linear permanent-magnet motor.
Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme (2015)

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the (1)H/(13)C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. (13)C and (1)H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.
Rapid Identification and Typing of Listeria Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (2008)

Listeria monocytogenes is a food-borne pathogen that is the causative agent of human listeriosis, an opportunistic infection that primarily infects pregnant women and immunologically compromised individuals. Rapid, accurate discrimination between Listeria strains is essential for appropriate therapeutic management and timely intervention for infection control. A rapid method involving matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that shows promise for identification of Listeria species and typing and even allows for differentiation at the level of clonal lineages among pathogenic strains of L. monocytogenes is presented. A total of 146 strains of different Listeria species and serotypes as well as clinical isolates were analyzed. The method was compared with the pulsed-field gel electrophoresis analysis of 48 Listeria strains comprising L. monocytogenes strains isolated from food-borne epidemics and sporadic cases, isolates representing different serotypes, and a number of Listeria strains whose genomes have been completely sequenced. Following a short inactivation/extraction procedure, cell material from a bacterial colony was deposited on a sample target, dried, overlaid with a matrix necessary for the MALDI process, and analyzed by MALDI-TOF MS. This technique examines the chemistry of major proteins, yielding profile spectra consisting of a series of peaks, a characteristic "fingerprint" mainly derived from ribosomal proteins. Specimens can be prepared in a few minutes from plate or liquid cultures, and a spectrum can be obtained within 1 minute. Mass spectra derived from Listeria isolates showed characteristic peaks, conserved at both the species and lineage levels. MALDI-TOF MS fingerprinting may have potential for Listeria identification and subtyping and may improve infection control measures.
Iterative learning control design for synchronization of wafer and reticle stages (2008)

This paper presents an iterative learning controller (ILC) design technique for synchronization in wafer scanning systems. In wafer scanners, synchronization of the wafer and reticle stages is critical for accurate pattern transfer. For synchronization, a master-slave configuration is used, with the wafer stage acting as the master, and the reticle stage as the slave. Since the scanning process is repetitive, ILC is used to improve tracking performance. However, the coupling between the reticle stage and wafer stage is unidirectional. Hence we propose an ILC scheme that takes into account this structural property of the overall system. A simple design procedure is presented which allows design of the ILC system for the wafer and reticle stages independently. This is done by first designing an ILC controller for the wafer (master) stage, and then using the synchronization error for ILC update for the reticle (slave) stage. Analytic conditions for stability and monotonic error convergence are then discussed. Finally, design and performance of the algorithm is illustrated by implementation on a single degree of freedom wafer stage, and a virtual (computer-simulated) reticle stage.
Robust control of quantum information (2003)

Errors in the control of quantum systems may be classified as unitary, decoherent, and incoherent. Unitary errors are systematic, and result in a density matrix that differs from the desired one by a unitary operation. Decoherent errors correspond to general completely positive superoperators, and can only be corrected using methods such as quantum error correction. Incoherent errors can also be described, on average, by completely positive superoperators, but can nevertheless be corrected by the application of a locally unitary operation that “refocuses” them. They are due to reproducible spatial or temporal variations in the system’s Hamiltonian, so that information on the variations is encoded in the system’s spatiotemporal state and can be used to correct them. In this paper liquid-state nuclear magnetic resonance is used to demonstrate that such refocusing effects can be built directly into the control fields, where the incoherence arises from spatial inhomogeneities in the quantizing static magnetic field as well as the radio-frequency control fields themselves. Using perturbation theory, it is further shown that the eigenvalue spectrum of the completely positive superoperator exhibits a characteristic spread that contains information on the Hamiltonians’ underlying distribution.
Erratum: Biogenic synthesis of Zinc oxide nanostructures from Nigella sativa seed: Prospective role as food packaging material inhibiting broad-spectrum quorum sensing and biofilm (2017)

Scientific Reports 6: Article number: 36761; published online: 05 December 2016; updated: 09 February 2017 The original version of this Article contained a typographical error in the spelling of Ali Alsalme, which was incorrectly given as Ali Mohammed Alsalme. In addition, Mohamed F. Al-Ajmi was incorrectly affiliated to “Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh-11451, Kingdom of Saudi Arabia”.
Association between dental factors and mortality (2020)

The number of missing teeth appeared to be the strongest predictor of mortality in this study, whereas endodontic infections per se had no independent association. Nevertheless, signs of professional intervention in these problems, such as root canal fillings and removable dentures, appeared to be associated with improved survival, which might partly be explained by the utilization of healthcare services.
[P2–378]: NEUROPSYCHOLOGICAL AND NEUROANATOMICAL CORRELATES OF EVENT‐RELATED POTENTIALS IN PATIENTS WITH ALZHEIMER's DISEASE (2017)

Discrimination of patients with Alzheimer's disease (AD) from age-matched healthy adults has been demonstrated using event-related potentials (ERP). In this study we investigated the associations between ERP measures from an oddball paradigm and regional gray matter (GM). A second study objective was to identify ERP measures that could reflect disease staging (in concordance with neuropsychological assessment and hippocampal atrophy). Sixty-two patients with mild AD (MMSE 21–26) were evaluated using a comprehensive neuropsychological assessment battery, an active auditory oddball ERP paradigm, and structural MRI. Voxel-based morphometry and cortical thickness (CT) assessment were used to quantify GM across multiple regions of interest. Correlation analyses assessed the relationship between the ERP measures (e.g., component amplitude and latency) and regions of interest. Accuracy in the oddball task was associated with CT within the anterior cingulate bilaterally and the left insula. Measures such as the Distractor and Standard N100 amplitudes (associated with detection of acoustic change) correlated positively with CT in the right supramarginal gyrus. Distractor P3a amplitude (linked with directing attention to novel stimuli) was positively correlated with CT within regions such as the anterior cingulate, the transverse temporal and superior temporal gyri. Target P3b amplitude (linked to attention/working memory) correlated with CT within regions such as the transverse and middle temporal gyri. In relation to disease staging, measures such as Distractor P3a amplitude were correlated with performance on the Alzheimer Disease Assessment Scale – cognitive subscale (ADAS-cog), whereas ERP components such as Distractor N100 latency, Standard P200 latency, Target P200 amplitude, and Slow Wave Target latency correlated with hippocampal volume. This study shows associations between a range of ERP components and GM in various brain regions in patients with mild AD. Knowledge of these associations offers greater insight into the neurophysiology behind the oddball ERP test and its applications in the detection of AD. In addition, we report correlations of ERP measures with hippocampal volume and neuropsychological tests. Given the simplicity of the ERP test and the demonstrated links to established measures for disease staging some of the ERP measures might be useful for patient monitoring.
Extracorporeal techniques for the treatment of critically ill patients with sepsis beyond conventional blood purification therapy: the promises and the pitfalls (2018)

Sepsis is one of the leading causes of morbidity and mortality worldwide. It is characterized by a dysregulated immune response to infections that results in life-threatening organ dysfunction and even death. Bacterial cell wall components (endotoxin or lipopolysaccharide), known as pathogen-associated molecular patterns (PAMPs), as well as damage-associated molecular patterns (DAMPs) released by host injured cells, are well-recognized triggers resulting in the elevation of both pro-inflammatory and anti-inflammatory cytokines. Understanding this complex pathophysiology has led to the development of therapeutic strategies aimed at restoring a balanced immune response by eliminating/deactivating these inflammatory mediators. Different extracorporeal techniques have been studied in recent years in the hope of maximizing the effect of renal replacement therapy in modulating the exaggerated host inflammatory response, including the use of high volume hemofiltration (HVHF), high cut-off (HCO) membranes, adsorption alone, and coupled plasma filtration adsorption (CPFA). These strategies are not widely utilized in practice, depending on resources and local expertise. The literature examining their use in septic patients is growing, but the evidence to support their use at this stage is considered of low level. Our aim is to provide a comprehensive overview of the technical aspects, clinical applications, and associated side effects of these techniques.
Brachyspira pilosicoli colonization in experimentally infected mice can be facilitated by dietary manipulation (2004)

The purpose of this study was to determine whether defined dietary manipulations would enhance colonization of mice experimentally challenged with the intestinal spirochaete Brachyspira pilosicoli. Weanling C3H/HeJ mice (n = 48) were fed either a standard balanced mouse diet or a diet supplemented with 50 p.p.m. zinc bacitracin (ZnB), with 50 % (w/w) lactose or with both supplements. Eight mice from each group were challenged orally with a human strain of B. pilosicoli (WesB), whilst four in each group acted as uninfected controls to evaluate the effects of the diets alone. The mice were kept for 40 days following challenge and faeces were collected every 3-4 days and subjected to culture and PCR for B. pilosicoli. Feeding ZnB reduced total volatile fatty acid production in the caecum. Feeding lactose alone doubled the weight of the caecum and its contents compared with control mice, and resulted in a relatively greater production of acetate, but a reduction in propionate and isovalerate production. These effects were negated by the addition of ZnB with the lactose. None of the mice fed the standard diet or receiving ZnB alone became colonized following experimental challenge. One of the mice receiving lactose was culture and PCR positive for B. pilosicoli on one sampling 1 week after inoculation, and one was positive on three samplings taken 20, 25 and 29 days after inoculation. All mice receiving both lactose and ZnB became colonized and remained so, with all samples being positive over the last seven samplings. The colonization was not associated with an end-on attachment of the spirochaete to the epithelial cells of the caecum, but colonized mice developed a specific humoral antibody response to the spirochaete.