gebhart/patrepeval huggingface dataset:
Emulsifying Activities of Purified Alasan Proteins from Acinetobacter radioresistens KA53 (2001)

The bioemulsifier of Acinetobacter radioresistens KA53, referred to as alasan, is a high-molecular-weight complex of polysaccharide and protein. The emulsifying activity of the purified polysaccharide (apo-alasan) is very low. Three of the alasan proteins were purified by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis and had apparent molecular masses of 16, 31, and 45 kDa. Emulsification assays using the isolated alasan proteins demonstrated that the active components of the alasan complex are the proteins. The 45-kDa protein had the highest specific emulsifying activity, 11% higher than the intact alasan complex. The 16- and 31-kDa proteins gave relatively low emulsifying activities, but they were significantly higher than that of apo-alasan. The addition of the purified 16- and 31-kDa proteins to the 45-kDa protein resulted in a 1.8-fold increase in the specific emulsifying activity and increased stability of the oil-in-water emulsion. Fast-performance liquid chromatography analysis indicated that the 45-kDa protein forms a dimer in nondenaturing conditions and interacts with the 16- and 31-kDa proteins to form a high-molecular-mass complex. The 45-kDa protein and the three-protein complex had substrate specificities for emulsification and a range of pH activities similar to that of alasan. The fact that the purified proteins are active emulsifiers should simplify structure-function studies and advance our understanding of their biological roles.
TGFβ Activated Kinase 1 (TAK1) at the Crossroad of B Cell Receptor and Toll-Like Receptor 9 Signaling Pathways in Human B Cells (2014)

B cell development and activation are regulated by combined signals mediated by the B cell receptor (BCR), receptors for the B-cell activating factor of the tumor necrosis factor family (BAFF-R) and the innate receptor, Toll-like receptor 9 (TLR9). However, the underlying mechanisms by which these signals cooperate in human B cells remain unclear. Our aim was to elucidate the key signaling molecules at the crossroads of BCR, BAFF-R and TLR9 mediated pathways and to follow the functional consequences of costimulation.Therefore we stimulated purified human B cells by combinations of anti-Ig, B-cell activating factor of the tumor necrosis factor family (BAFF) and the TLR9 agonist, CpG oligodeoxynucleotide. Phosphorylation status of various signaling molecules, B cell proliferation, cytokine secretion, plasma blast generation and the frequency of IgG producing cells were investigated. We have found that BCR induced signals cooperate with BAFF-R- and TLR9-mediated signals at different levels of cell activation. BCR and BAFF- as well as TLR9 and BAFF-mediated signals cooperate at NFκB activation, while BCR and TLR9 synergistically costimulate mitogen activated protein kinases (MAPKs), ERK, JNK and p38. We show here for the first time that the MAP3K7 (TGF beta activated kinase, TAK1) is responsible for the synergistic costimulation of B cells by BCR and TLR9, resulting in an enhanced cell proliferation, plasma blast generation, cytokine and antibody production. Specific inhibitor of TAK1 as well as knocking down TAK1 by siRNA abrogates the synergistic signals. We conclude that TAK1 is a key regulator of receptor crosstalk between BCR and TLR9, thus plays a critical role in B cell development and activation.
An orthogonal family of quincunx wavelets with continuously adjustable order (2005)

We present a new family of two-dimensional and three-dimensional orthogonal wavelets which uses quincunx sampling. The orthogonal refinement filters have a simple analytical expression in the Fourier domain as a function of the order lamda, which may be noninteger. We can also prove that they yield wavelet bases of L2(R2) for any lambda > 0. The wavelets are fractional in the sense that the approximation error at a given scale a decays like O(a(lamda)); they also essentially behave like fractional derivative operators. To make our construction practical, we propose a fast Fourier transform-based implementation that turns out to be surprisingly fast. In fact, our method is almost as efficient as the standard Mallat algorithm for separable wavelets.
Kinetic stability as a mechanism for protease longevity (1999)

The folding of the extracellular serine protease, alpha-lytic protease (alphaLP; EC 3.4.21.12) reveals a novel mechanism for stability that appears to lead to a longer functional lifetime for the protease. For alphaLP, stability is based not on thermodynamics, but on kinetics. Whereas this has required the coevolution of a pro region to facilitate folding, the result has been the optimization of native-state properties independent of their consequences on thermodynamic stability. Structural and mutational data lead to a model for catalysis of folding in which the pro region binds to a conserved beta-hairpin in the alphaLP C-terminal domain, stabilizing the folding transition state and the native state. The pro region is then proteolytically degraded, leaving the active alphaLP trapped in a metastable conformation. This metastability appears to be a consequence of pressure to evolve properties of the native state, including a large, highly cooperative barrier to unfolding, and extreme rigidity, that reduce susceptibility to proteolytic degradation. In a test of survival under highly proteolytic conditions, homologous mammalian proteases that have not evolved kinetic stability are much more rapidly degraded than alphaLP. Kinetic stability as a means to longevity is likely to be a mechanism conserved among the majority of extracellular bacterial pro-proteases and may emerge as a general strategy for intracellular eukaryotic proteases subject to harsh conditions as well.
Initial results from the Magellan stereo experiment (1992)

The second global radar image coverage of Venus by Magellan included a 1 day experiment to produce a set of eight images along orbits that combined with the original nominal imagery into stereo image pairs suited for visual stereo interpretation and mapping of topographic elevations. Initial analysis shows excellent stereo radar data with good vertical exaggeration of six and more, parallax accuracies of ±0.6 pixels or ±45 m and a surface definition within ±30 m. The topographic relief can be very accentuated, with local elevation differences of 2.5 km and terrain slopes often in excess of 25°. This data set has proven the usefulness of global stereo coverage and marks the beginning of significant planetary stereo radargrammetric developments. Extensive mapping with this same stereo geometry is being carried out in cycle 3, and preparations are underway to develop a detailed stereo radargrammetric topographic model of the planet.
3D localization of implanted radioactive sources in the prostate using trans-urethral ultrasound. (2001)

Prostate cancer is the most common cancer diagnosed in men in the United States. Many techniques have been developed to diagnose and treat prostate cancer. 3D Trans-Urethral Ultrasound (TUUS) is a new technique for the diagnosis and treatment of prostate disease. This research focuses on the potential of TUUS for therapy-guidance during and after transperineal interstitial permanent prostate brachytherapy (TIPPB). Computed tomography (CT) is currently used to determine the source locations and the effective radiation dose distribution throughout the tissue after the completion of the procedure. TUUS may be a viable alternative to CT for determining source locations within the prostate. Placement of the TUUS catheter into the urethra provides excellent 2D images of the prostate. In addition, the catheter can be used to acquire 3D volumetric data for 3D analysis of the prostate, associated tissue, and radioactive sources. Initial work on source localization was conducted on an ultrasound-equivalent prostate phantom. Cylindrical dummy radiation sources with diameter of .8 mm and length of 4.5 mm were placed into the prostate phantom for assessment with TUUS. The TUUS imaging device is a 10 fr catheter with a linear array of ultrasonic crystals at one end. The ultrasound catheter operates at 10 MHz and is controlled by the Acuson Sequoia ultrasound workstation. The catheter was placed in the phantom urethra and 3D scans were acquired. A corresponding CT was acquired for comparative purposes. Segmentation of the prostate capsule was done semi-automatically. Dummy radiation seed segmentation was conducted manually. Additional processing was necessary to account for image artifact and correctly reconstruct the seeds. The prostate shell and radioactive source reconstructions provide an excellent 3D representation. Comparison to the CT data suggests that the TUUS data provided: 1) greater resolution and 2) better soft tissue differentiation. The reconstructed sources were measured and corresponded to the physical dimensions of those placed in the phantoms. The method is now being evaluated on cadavers and patients.
Assessment of the Foot and Ankle in Elite Athletes (2009)

An accurate assessment of the foot and ankle problem in elite athletes is the foundation of a treatment plan and prognosis. The special pressures of professional sports, where managers, agents, and lawyers may be involved, makes a thorough assessment especially critical for sound decision-making. Evaluation includes taking a history of the acute and chronic condition, including mechanism, physical sensation at injury, compensatory stresses, and general medical review. The athlete is assessed physically in several different ways, including comprehensive focal examination and alignment in static and dynamic nonweight-bearing and weight-bearing modes. This comprehensive process is essential to accurate assessment.
Target discrimination in the extended shortwave infrared band (2 to 2.5μm) compared with visible, near-infrared, and SWIR in degraded visual environments (2022)

Long-range target identification is well studied in the visible (Vis) and near-infrared (NIR) bands and more recently in the shortwave infrared (SWIR). The longer wavelength of SWIR (1 to 1.7 μm) improves target detection for both long ranges and under challenging atmospheric conditions because it is less limited by scattering and absorption in the atmosphere. For these reasons, SWIR sensors are proliferating on military platforms. The extended shortwave infrared (eSWIR) band spanning from 2 to 2.5 μm is not typically limited by diffraction, and as a result, the band benefits target acquisition both at long ranges and for degraded visual environments (DVEs). Theoretical and experimental data compare eSWIR with Vis, NIR, and SWIR for atmospheric transmission, reflectivity, illumination, and sensor resolution and sensitivity. The experimental setup includes two testbeds, each with four cameras. The first is a wide field of view (FOV) testbed matching FOV at 20 deg for each camera. The second is a narrow FOV telescope testbed to match instantaneous FOV for consistent resolution across all four bands at long ranges. Both the theory and experiment demonstrate advantages of using eSWIR for long-range target identification under DVEs.
ChemInform Abstract: Korormicin, a Novel Antibiotic Specifically Active Against Marine Gram‐Negative Bacteria, Produced by a Marine Bacterium. (1998)

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.
Compression Characterization and Lubricant Sensitivity of Orally Disintegrating Tablets Based on Ludiflash (2008)

excipient designed for orally dispersible tablets – was recently introduced into the market enabling quick development and cost-effective production of orally dispersible tablet via direct compression [1]. Because of its composition and physical structure it combines fast disintegration times with high hardness and a very smooth mouthfeel.� This study describes the impact of lubricant type and compression settings on tablet properties. As lubricants magnesium stearate and sodium stearyl fumarate, which differ strongly in lipophilicity were used. In addition the chosen placebo formulation was compressed on two tablet presses – one with and one without precompression roll. The goal was to optimize the composition and the manufacturing process of tablets based on Ludiflash®.
Programmed Self-Assembly of an Active P22-Cas9 Nanocarrier System (2016)

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) RNA-guided endonucleases are powerful new tools for targeted genome engineering. These nucleases provide an efficient and precise method for manipulating eukaryotic genomes; however, delivery of these reagents to specific cell-types remains challenging. Virus-like particles (VLPs) derived from bacteriophage P22, are robust supramolecular protein cage structures with demonstrated utility for cell type-specific delivery of encapsulated cargos. Here, we genetically fuse Cas9 to a truncated form of the P22 scaffold protein, which acts as a template for capsid assembly as well as a specific encapsulation signal for Cas9. Our results indicate that Cas9 and a single-guide RNA are packaged inside the P22 VLP, and activity assays indicate that this RNA-guided endonuclease is functional for sequence-specific cleavage of dsDNA targets. This work demonstrates the potential for developing P22 as a delivery vehicle for cell specific targeting of Cas9.
Cutting-edge techniques for molecular imaging with relevance to therapeutic delivery methods (2013)

Molecular imaging methods and techniques have been the subject of considerable recent interest in therapeutics due to their noninvasive nature and their inherent importance for the efficient performance of various guided, targeted and responsive therapeutic delivery systems. These ‘theranostics’ are particularly applicable to rapidly proliferating conditions, such as tumor-related issues and pulmonary diseases, as they can provide for noninvasive objective diagnosis, image-guided and targeted treatment, and monitoring of the therapies via nanomedicinal interventions and nanodiagnostic tools [1,2].
Development and Validation of Non-Integrative, Self-Limited, and Replicating Minicircles for Safe Reporter Gene Imaging of Cell-Based Therapies (2013)

Reporter gene (RG) imaging of cell-based therapies provides a direct readout of therapeutic efficacy by assessing the fate of implanted cells. To permit long-term cellular imaging, RGs are traditionally required to be integrated into the cellular genome. This poses a potential safety risk and regulatory bottleneck for clinical translation as integration can lead to cellular transformation. To address this issue, we have developed non-integrative, replicating minicircles (MCs) as an alternative platform for safer monitoring of cells in living subjects. We developed both plasmids and minicircles containing the scaffold/matrix attachment regions (S/MAR) of the human interferon-beta gene, driven by the CMV promoter, and expressing the bioluminescence RG firefly luciferase. Constructs were transfected into breast cancer cells, and expanded S/MAR minicircle clones showed luciferase signal for greater than 3 months in culture and minicircles remained as episomes. Importantly, luciferase activity in clonal populations was slowly lost over time and this corresponded to a loss of episome, providing a way to reversibly label cells. To monitor cell proliferation in vivo, 1.5 × 10(6) cells carrying the S/MAR minicircle were implanted subcutaneously into mice (n = 5) and as tumors developed significantly more bioluminescence signal was noted at day 35 and 43 compared to day 7 post-implant (p<0.05). To our knowledge, this is the first work examining the use of episomal, self-limited, replicating minicircles to track the proliferation of cells using non-invasive imaging in living subjects. Continued development of S/MAR minicircles will provide a broadly applicable vector platform amenable with any of the numerous RG technologies available to allow therapeutic cell fate to be assessed in individual patients, and to achieve this without the need to manipulate the cell's genome so that safety concerns are minimized. This will lead to safe tools to assess treatment response at earlier time points and improve the precision of cell-based therapies.
How can you trust what you read? (2023)

<i>Chemical Science</i> is introducing the option of transparent peer-review for authors. Editor-in-Chief Andy Cooper and Executive Editor May Copsey take a look at the reasons why, and how this will work.
The Effect of Leukocyte Hydrolases on Bacteria. III. Bacteriolysis Induced by Extracts of Different Leukocyte Populations and the Inhibition of Lysis by Macromolecular Substances (1975)

The lysis of 14C-labeled bacteria by hydrolases of human and rabbit leukocytes was studied in vitro. While Staphylococcus albus, Streptococcus faecalis, and Streptococcus mutans were highly susceptible to lysis, Staphylococcus auresus was intermediate in its susecptibility to lysis by the leukocyte enzymes. Group A Streptococcus, Listeria monocytogenes, Shigella flexneri, Escherichia coli, and Mycobacterium smegmatis were very resistant to degradation by these enzymes. The lytic activity of leukocyte lysates from human and rabbit blood was probably due to acid hydrolases of polymorphonuclear leukocytes. Extracts of human blood monocytes and of rabbit peritoneal and lung macrophages were less lytic for the bacteria tested. Lymphocytes and platelet extracts were not bacteriolytic. The lytic effect of the leukocyte lysates was not inhibited by KCN or sodium azide, but was abolished to a large extent by cationic polyelectrolytes such as protamine sulfate, histone and leukocyte cationic proteins, and poly-lysine, as well as by the anionic polyelectrolytes such as heparin, chondroitin sulfate, DNA, carrageenin, alginate sulfate, dextran sulfate, and ploy-L-glutamic acid. Other potent inhibitors of bacteriolysis were trypan blue, congo red, phosphatidic acid, normal immunoglobulins, and components of streptococcal cell wall.
Large system analysis of the secrecy sum-rates with Regularized Channel Inversion precoding (2012)

In this paper, we study the performance of the Regularized Channel Inversion (RCI) precoder in a multi-user MIMO system with malicious users. We consider the general case when the number of users per transmit antenna β can take any value. We derive the optimal regularization parameter that maximizes the achievable secrecy sum-rate via large-system analysis, which we show to be accurate via simulations. We find that the secrecy requirements limit the number of users per transmit antenna that can be served with non-zero sum-rate. We show that for large signal-to-noise ratio, RCI can achieve secrecy without reducing the sum-rate if β <; 1. If β = 1, this is still possible at a cost of less than 4dB in terms of transmitted power. If β >; 1, then the secrecy requirements result in a poor sum-rate.
Dynamics of a hollow cathode discharge in the frequency range of 1–500 kHz (2020)

Abstract We present results from 2D axisymmetric fluid simulations of the partially-ionized Xe gas in a 25-A cathode discharge, for a range of flow rates (5–20 sccm) in which transition between the so-called spot and plume modes has been observed in laboratory experiments. The simulations for the first time capture very well the characteristic rise of the peak-to-peak amplitude in the keeper voltage oscillations with decreasing flow rate — the so-called ‘plume margin’ — thereby allowing for a closer interrogation of the processes that drive them. The oscillations are found to be due to plasma dynamics in the near-plume region that increase in amplitude as the flow rate is reduced. The cathode interior remains largely quiescent and changes in the emitter peak temperature do not exceed 2% across the entire range of flow rates examined. Along the cathode centerline the amplitude of the electron density oscillations peak at a location where the number density of the Xe atoms has diminished to its minimum value and the degree of ionization is close to one. The computed spectra reveal that most of the oscillation power resides in the frequency range of 100–300 kHz. These frequencies are much greater than the local ionization collision frequency ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi>ν</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="bold">e</mml:mi> <mml:mi mathvariant="bold">A</mml:mi> </mml:mrow> <mml:mrow> <mml:mi mathvariant="bold">I</mml:mi> </mml:mrow> </mml:msubsup> </mml:math> &lt; 10 kHz), and are associated with wavelengths of several centimeters. Such wavelengths are many orders of magnitude greater than λ D . The waves are largely longitudinal with wave vector in the axial direction, and phase velocity ω / k &gt; 10 km s −1 , which is more than 6× greater than the ion acoustic speed. Though the computed and measured plume margins are in good agreement the measured spectra show that most of the power resides between ∼60 and 90 kHz, lower than the computed range (100–300 kHz), and exhibits a sharper distribution. It is argued this is due to the presence of a rotational mode in the experiment that is coupled with the longitudinal mode, yielding a complex 3D plasma motion that cannot be captured by the simulations due to the assumption of azimuthal axisymmetry, but that it is indeed the longitudinal plasma motion that drives the transition from spot to plume modes. An anomalous resistivity has been invoked in the simulations that is based on the formulations of Sagdeev and Galeev for the saturation of IAT which is long known to exist in these discharges. Though the simulations do not account for possible anomalous heating of the ions, the idealized model for the electrons is found to be sufficient in capturing the abovementioned dynamics, yielding a multiplication coefficient α of the anomalous collision frequency ν α = αω pe ( T e / T i )( u e / u Te ) that is within a factor of two of the estimated theoretical value.
The effect of the antisperm auto-antibody-bound sperm on in vitro fertilization outcome (2009)

To evaluate the effects of antisperm auto-antibody-bound sperm on the outcome of in vitro fertilization-embryo transfer (IVF-ET), 160 infertile couples undergoing treatment by in vitro fertilization were recruited in this study. In the study group (11 couples, 15 cycles), the male partners were positive for antisperm autoantibodies determined by immunobead test (IBT). In the control group (149 couples, 152 cycles), the men had no such antibodies. The percentages of fertilization rate, cleavage rate and pregnancy rate of the study group and control group wer 75.0 +/- 5.2% vs. 69.3 +/- 2.4%; 82.8% +/- 3.7% and 6.7% +/- 11.8%, respectively. There were no significant differences in in vitro region, type and/or percentage of sperm-bound antibodies also had no effect on the in vitro fertilization outcome. In conclusion, in vitro fertilization-embryo transfer is not significantly affected by antisperm autoantibody-bound sperm determined by immunobead test.