gebhart/patrepeval huggingface dataset:
Particle Formation in Ambient MALDI Plumes (2011)

The ablated particle count and size distribution of four solid matrix materials commonly used for matrix-assisted laser desorption ionization (MALDI) were measured with a scanning mobility particle sizer (SMPS) combined with a light scattering aerodynamic particle sizer (APS). The two particle sizing instruments allowed size measurements in the range from 10 nm to 20 μm. The four solid matrixes investigated were 2,5-dihydroxybenzoic acid (DHB), 4-nitroaniline (NA), α-cyano-4-hydroxycinnamic acid (CHCA), and sinapic acid (SA). A thin film of the matrix was deposited on a stainless steel target using the dried droplet method and was irradiated with a 337 nm nitrogen laser at atmospheric pressure. The target was rotated during the measurement. A large number of nanoparticles were produced, and average particle diameters ranged from 40 to 170 nm depending on the matrix and the laser fluence. These particles are attributed to agglomeration of smaller particles and clusters and/or hydrodynamic sputtering of melted matrix. A coarse particle component of the distribution was observed with diameters between 500 nm and 2 μm. The coarse particles were significantly lower in number but had a total mass that was comparable to that of the nanoparticles. The coarse particles are attributed to matrix melting and spallation. Two of the compounds, CHCA and SA, had a third particle size distribution component in the range of 10 to 30 nm, which is attributed to the direct ejection of clusters.
Inhibition of Human Immunodeficiency Virus Type 1 gp120 Presentation to CD4 T Cells by Antibodies Specific for the CD4 Binding Domain of gp120 (2001)

Human immunodeficiency virus (HIV)-specific CD4 T-cell responses, particularly to the envelope glycoproteins of the virus, are weak or absent in most HIV-infected patients. Although these poor responses can be attributed simply to the destruction of the specific CD4 T cells by the virus, other factors also appear to contribute to the suppression of these virus-specific responses. We previously showed that human monoclonal antibodies (MAbs) specific for the CD4 binding domain of gp120 (gp120(CD4BD)), when complexed with gp120, inhibited the proliferative responses of gp120-specific CD4 T-cells. MAbs to other gp120 epitopes did not exhibit this activity. The present study investigated the inhibitory mechanisms of the anti-gp120(CD4BD) MAbs. The anti-gp120(CD4BD) MAbs complexed with gp120 suppressed gamma interferon production as well as proliferation of gp120-specific CD4 T cells. Notably, the T-cell responses to gp120 were inhibited only when the MAbs were added to antigen-presenting cells (APCs) during antigen pulse; the addition of the MAbs after pulsing caused no inhibition. However, the anti-gp120(CD4BD) MAbs by themselves, or as MAb/gp120 complexes, did not affect the presentation of gp120-derived peptides by the APCs to T cells. These MAb/gp120 complexes also did not inhibit the ability of APCs to process and present unrelated antigens. To test whether the suppressive effect of anti-gp120(CD4BD) antibodies is caused by the antibodies' ability to block gp120-CD4 interaction, APCs were treated during antigen pulse with anti-CD4 MAbs. These treated APCs remained capable of presenting gp120 to the T cells. These results suggest that anti-gp120(CD4BD) Abs inhibit gp120 presentation by altering the uptake and/or processing of gp120 by the APCs but their inhibitory activity is not due to blocking of gp120 attachment to CD4 on the surface of APCs.
Lumbar Plexus Anatomy within the Psoas Muscle: Implications for the Transpsoas Lateral Approach to the L4-L5 Disc (2011)

Because of the proximity of the neural elements, in particular the femoral nerve, to the center of the disc space, the transpsoas lateral surgical approach to the L4-L5 disc space will likely cause intraoperative displacement of neural structures from their anatomic course during retractor dilation. Careful attention should be paid to retractor placement and dilation time during transpsoas lateral access surgery, particularly at the L4-L5 disc.
Opportunistic Multiuser Two-Way Amplify-and-Forward Relaying With a Multiantenna Relay (2015)

We consider the opportunistic multiuser diversity in the multiuser two-way amplify-and-forward (AF) relay channel. The relay, which is equipped with multiple antennas and a simple zero-forcing beamforming (ZFBF) scheme, selects a set of two way relaying user pairs to enhance the degree of freedom (DoF) and, consequently, the sum throughput of the system. The proposed channel-aligned pair scheduling (CAPS) algorithm reduces the interpair interference and keeps the signal-to-interference-plus-noise-power ratio (SINR) of user pairs that are interference-free when the number of user pairs becomes very large. When the number of user pairs grows fast enough with the system signal-to-noise ratio (SNR), a DoF equal to the number of relay antennas can be achieved. For a realistic number of user pairs, we propose an adaptive CAPS and an adaptive semi-orthogonal CAPS (SCAPS) to improve performance. Simulation results show that adaptive CAPS and adaptive SCAPS provide throughput gain in the low-to-mid SNR region.
Non-planar pad-printed thick-film focused high-frequency ultrasonic transducers for imaging and HIFU applications (2011)

Most high-frequency ultrasound transducers for imaging applications are based either on piezopolymers or on lapped bulk piezoceramics. The latter are planar, so focusing can be obtained by adding a lens (at the price of lower sensitivity) or by fracturing into a curved geometry. Pad printed thick-film transducers have been shown to be an interesting alternative, namely because the film is deposited with the required thickness, size and geometry, thus avoiding any subsequent machining and allowing geometrical focusing to be achieved. Film electromechanical properties are close to those of bulk ceramics with similar composition despite higher porosity. In this paper, pad-printed high-frequency transducers based on a low-loss piezoceramic composition are designed and fabricated. High-porosity ceramic cylinders with a spherical top surface are used as substrates and serve as backing material. The transducers are first characterized in view of imaging applications using a short pulse excitation, and their imaging capabilities are evaluated. Secondly, the transducers are excited by a one-period sine wave using several power levels to evaluate their capability to produce high-intensity focused ultrasound (HIFU) at frequencies around 20 MHz. The results, obtained via hydrophone measurements, are discussed showing that transducer performance is promising for applications that would require the same device to be used for imaging and for therapy. Nevertheless, the transducer design can be improved, and simulation studies are performed in order to find a better compromise between low-power and high-power performance. The size, geometry and constitutive materials of optimized configurations are proposed and their feasibility is discussed.
Clinical approval of nanotechnology-based SARS-CoV-2 mRNA vaccines: impact on translational nanomedicine (2021)

One year after the first human case of SARS-CoV-2, two nanomedicine-based mRNA vaccines have been fast-tracked, developed, and have received emergency use authorization throughout the globe with more vaccine approvals on the heels of these first two. Several SARS-CoV-2 vaccine compositions use nanotechnology-enabled formulations. A silver lining of the COVID-19 pandemic is that the fast-tracked vaccine development for SARS-CoV-2 has advanced the clinical translation pathway for nanomedicine drug delivery systems. The laboratory science of lipid-based nanoparticles was ready and rose to the clinical challenge of rapid vaccine development. The successful development and fast tracking of SARS-CoV-2 nanomedicine vaccines has exciting implications for the future of nanotechnology-enabled drug and gene delivery; it demonstrates that nanomedicine is necessary and critical to the successful delivery of advanced molecular therapeutics such as nucleic acids, it is establishing the precedent of safety and the population effect of phase four clinical trials, and it is laying the foundation for the clinical translation of more complex, non-lipid nanomedicines. The development, fast-tracking, and approval of SARS-CoV-2 nanotechnology-based vaccines has transformed the seemingly daunting challenges for clinically translating nanomedicines into measurable hurdles that can be overcome. Due to the tremendous scientific achievements that have occurred in response to the COVID-19 pandemic, years, perhaps even decades, have been streamlined for certain translational nanomedicines.
Link failure detection in a parallel computer (2023)

Methods, apparatus, and products are disclosed for link failure detection in a parallel computer including compute nodes connected in a rectangular mesh network, each pair of adjacent compute nodes in the rectangular mesh network connected together using a pair of links, that includes: assigning each compute node to either a first group or a second group such that adjacent compute nodes in the rectangular mesh network are assigned to different groups; sending, by each of the compute nodes assigned to the first group, a first test message to each adjacent compute node assigned to the second group; determining, by each of the compute nodes assigned to the second group, whether the first test message was received from each adjacent compute node assigned to the first group; and notifying a user, by each of the compute nodes assigned to the second group, whether the first test message was received.
Polymyxin B nonapeptide: Conformations in water and in the lipopolysaccharide-bound state determined by two-dimensional NMR and molecular dynamics (1997)

Polymyxin B nonapeptide (PMN) is a derivative of polymyxin B, an α, γ-diaminobutyric acid-rich decapeptide from Bacillus polymyxa that displays antimicrobial and lipopolysaccharide (LPS)-antagonistic activities. The conformations of PMN in aqueous solution as well as in the LPS-bound state have been studied by 1H two-dimensional nmr methods in conjunction with molecular dynamics techniques. The aqueous structure of the free peptide is characterized by a type II′ β-turn centered around D-Phe5 and Leu6, and an inverse γ-turn at Thr9. The LPS-bound conformation of PMN was studied by transferred nuclear Overhauser effect experiments. The essential features of the cyclic portion of free aqueous PMN are mostly preserved when the peptide is bound to LPS; however, the linear dipeptide fragment as well as the side chains of the heptatpeptide ring show a conformational change and a reduction in mobility. The LPS-bound PMN structure was used to construct a model of the lipid A-polymyxin B (decapeptide) complex, which allows the rationalization of several experimental observations concerning the binding of polymyxin to, and consequent neutralization of, the toxicity of LPS, and may be of value in the rational therapeutic targeting of endotoxin. © 1997 John Wiley & Sons, Inc.
Immunological Origins of Binding and Catalysis in a Diels-Alderase Antibody (1998)

The three-dimensional structure of an antibody (39-A11) that catalyzes a Diels-Alder reaction has been determined. The structure suggests that the antibody catalyzes this pericyclic reaction through a combination of packing and hydrogen-bonding interactions that control the relative geometries of the bound substrates and electronic distribution in the dienophile. A single somatic mutation, serine-91 of the light chain to valine, is largely responsible for the increase in affinity and catalytic activity of the affinity-matured antibody. Structural and functional studies of the germ-line precursor suggest that 39-A11 and related antibodies derive from a family of germ-line genes that have been selected throughout evolution for the ability of the encoded proteins to form a polyspecific combining site. Germ line-encoded antibodies of this type, which can rapidly evolve into high-affinity receptors for a broad range of structures, may help to expand the binding potential associated with the structural diversity of the primary antibody repertoire.
Supplementary Figures S1-S12 and Supplementary Tables S1-S3 from Novel Glycosylated VEGF Decoy Receptor Fusion Protein, VEGF-Grab, Efficiently Suppresses Tumor Angiogenesis and Progression (2023)

&lt;p&gt;Supplementary Figure S1. Sequence Alignment of VEGF-Grab1, VEGF-Grab3, and VEGF-Trap; Supplementary Figure S2. Analysis of N-linked Glycosylation for VEGF-Grabs and VEGF-Trap; Supplementary Figure S3. Analysis of O-linked Glycosylation in VEGF-Grab1; Supplementary Figure S4. VEGF-Grab3 displays low binding to tumor ECM; Supplementary Figure S5. Pharmacokinetic profile of VEGF-Grab1 and VEGF-Grab3; Supplementary Figure S6. Tissue accumulation of VEGF-Trap and VEGF-Grab3; Supplementary Figure S7. VEGF-Grabs or VEGF-Trap have no effects on VEGFR2 signalling, EC survival, migration, and tube formation in the absence of VEGFA; Supplementary Figure S8. Dose-dependent Inhibition of VEGFR2 Signalling with Anti-VEGF Therapy; Supplementary Figure S9. Histologic Analyses of Vital Organs after Anti-VEGF Therapy; Supplementary Figure S10. VEGF-Grab effectively suppresses the growth of established bulky macroscopic tumors; Supplementary Figure S11. Histological analyses of the kidney and liver after dose dependent anti-VEGF therapy; Supplementary Figure S12. Combination Therapy of VEGF-Grab3 and Cisplatin Enhances Intratumoral Apoptosis; Supplementary Table S1. Primer sequences for site-directed mutagenesis; Supplementary Table S2. Primer sequences for Quantitative Real Time PCR; Supplementary Table S3. Antibodies.&lt;/p&gt;
Bias Correction of Learned Generative Models using Likelihood-Free Importance Weighting (2019)

A learned generative model often produces biased statistics relative to the underlying data distribution. A standard technique to correct this bias is importance sampling, where samples from the model are weighted by the likelihood ratio under model and true distributions. When the likelihood ratio is unknown, it can be estimated by training a probabilistic classifier to distinguish samples from the two distributions. We employ this likelihood-free importance weighting method to correct for the bias in generative models. We find that this technique consistently improves standard goodness-of-fit metrics for evaluating the sample quality of state-of-the-art deep generative models, suggesting reduced bias. Finally, we demonstrate its utility on representative applications in a) data augmentation for classification using generative adversarial networks, and b) model-based policy evaluation using off-policy data.
Champions in Our Midst: Immink helped jump-start the digital video and audio revolution (2014)

Welcome to a new series of articles for IEEE Consumer Electronics Magazine. One of the benefits of joining the IEEE Consumer Electronics (CE) Society is that you get access to senior engineers and researchers from our industry. They are often at our conferences, workshops, and local Chapter meetings and frequently play an active role in the organization of Society activities.
BD/DVD/CD compatible objective lens (2006)

We have developed an objective lens which can be used for different optical disk formats -Blu-ray Disc, DVD and CD. The compatible technique is based on the diffraction characteristics optimized by tuning refractive index dispersion. This optical configuration can provide suitable designs for optical pick-up system of high speed recording.
G(AKSL2): a new cell surface antigen of the mouse related to the dualtropic mink cell focus-inducing class of murine leukemia virus detected by naturally occurring antibody. (1979)

Normal mouse sera were tested for cytotoxic antibody to surface antigens of cultured monolayer cells infected with AKR-derived ecotropic MuLV, xentropic MuLV, or dualtropic MCF 247 MuLV. Antibody to ecotropic MuLV-infected cells was found in a proportion of C57BL/6, C3Hf/Bi, AKR-Fv-1b, and (C3Hf/Bi X AKR)F1 mice, but not AKR or (AKR X C3Hf/Bi)F1 mice. Antibody to xenotropic MuLV-infected cells was virtually restricted to C57BL/6 mice. Antibody to MCF 247-infected cells was found in all strains tested, including AKR mice. Absorption analysis of (C3Hf/Bi x akr)f1 and AKR-Fv-1b sera with selective reactivity for MCF 247-infected cells showed that these sera recognize distinctive antigens on MCF 247-infected cells that are not present on ecotropic or xenotropic MuLV-infected cells. The transplantable AKR spontaneous leukemia AKSL2 was found to be uniquely sensitive to the cytotoxic action of naturally occurring antibody to MCF 247-related antigens and absorption tests with AKSL2 as the target cell and sera from a single AKR-Fv-1b mouse have permitted the definition of a new MuLV-related cell surface antigen, which has been designated G(AKSL2). Thymocytes from young mice of high leukemia-incidence strains (AKR, C58, and PL) express G(AKSL2), whereas thymocytes from 12 other strains do not. In AKR mice, the antigen is expressed in higher amounts on cells from thymus and bone marrow than on spleen cells. All AKR spontaneous leukemias tested express G(AKSL2), as did three MuLV-induced leukemias arising in G(AKSL2)- strains. Five X-ray-induced leukemias of G(AKSL2)- strains were G(AKSL2)-, as were MuLV+ and MuLV- chemically induced sarcomas. In the limited survey conducted to date, natural antibody to G(AKSL2) has been restricted to strains expressing G(AKSL2) in their normal tissues: AKR, AKR congenic mice AKR-Fv-1b and AKR hybrid mice (C3Hf/Bi x akr)f1 and (C57BL/6 X AKR)F1. In vitro G(AKSL2) induction tests involving MuLV infection of cultured monolayer cells showed that 8 of 12 newly isolated dualtropic MuLV shared the property of G(AKSL2) induction with the prototype MCF MuLV, MCF 247. Of the 12 ecotropic MuLV tested, only the N-tropic MuLV isolated from a leukemia originally induced by Passage A Gross virus induced G(AKSL2). The xenotropic and amphotropic MuLV isolates tested lacked G(AKSL2) inducing activity. Recognition of the g(aksl2) system provides a way to trace the origin and natural history of a class of dualtropic MCF MuLV in the mouse and to determine whether natural antibody to G(AKSL2) plays a role in AKR leukemogenesis.
Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids (1996)

Current “second-generation” force fields have been developed for use in Monte Carlo and molecular dynamics simulations for organic and biomolecular systems in solution. The performance of three such force fields, AMBER94, MMFF94, and OPLS-AA, is tested here through Monte Carlo (MC) statistical mechanics simulations for liquid butane, methanol, and N-methylacetamide (NMA). These liquids were chosen for their range of polarity and their representation of typical interactions found in proteins. From simulations at constant temperature and 1 atm pressure, the average errors in the computed densities and heats of vaporization are 3.8% and 5.1% with AMBER94 and 1.5% and 1.3% with OPLS-AA. With MMFF94, the computed densities and heats of vaporization for methanol and NMA are too low by 21−27%, while butane at −0.5 °C does not stop expanding during the simulation. A MC simulation using MMFF94 for butane with the density fixed at the experimental value yields a 32% error in the energy of vaporization. Analyses show that the optimal C−H and H−H nonbonded interactions with MMFF94 are too weak and occur at too large separations. Scaling of the MMFF94 parameter Ai, which is linearly related to the atomic radii, by 0.92 yields improved results for liquid butane.
Carbon Nanotube Mask Filters and Their Hydrophobic Barrier and Hyperthermic Antiviral Effects on SARS-CoV-2 (2021)

Carbon nanotube face mask filters have strong and uniform hydrophobicity, high durability, and high thermal conductivity and exhibit excellent barrier and antiviral effects against SARS-CoV-2. The nanocarbon filter functions as a superior barrier compared to those in conventional masks owing to the stronger, more uniform, and more durable hydrophobic nature of the carbon nanotubes. A tightly knit carbon nanotube network has a pore size smaller than that of the average coronavirus; nevertheless, the breathability is equal to that of the conventional polypropylene filter. The exceptional thermal conductivity of carbon nanotubes transpires hyperthermic antiviral effects, which offers stronger protection against the virus, as well as reusability. The facile processability, low cost, and light weight of the aerosol-synthesized carbon nanotube filter warrants its viability, reinforcing the fight against the COVID-19 pandemic.
Photoresist development as a reaction-diffusion process (Conference Presentation) (2019)

Development of a photoresist is a complex physical process involving solid-to-liquid solution phase transition where a developer solution dissolves a section of a patterned resist. The developer can be selective towards either the exposed region (positive-tone) or the unexposed region (negative-tone). Accurate estimation of the development effects is crucial to the prediction of critical dimension (CD) in lithography simulations. Traditionally, the development effects have been captured by a front-propagation equation (such as Mack model and other similar models), which features a development front with a velocity dependent on the resist’s de-protection level. For a positive-tone development (PTD), due to the aqueous nature of the developer, where an exposed part of resist quickly dissolves when in contact with a developer, such a moving front simulates the development process accurately. However, in case of a negative-tone development (NTD), the rate of reaction and resist contrast is significantly lower than for PTD. Therefore it is important to take into account both the developer’s finite diffusion into resist and its reaction rate with the resist to reliably model the development process. In this paper, we discuss the mathematical model of resist’s development by taking into account the transport phenomena of diffusion and reaction taking place during the development step. The finite-element method is used to solve these reaction-diffusion equations over the non-trivial geometry of a patterned resist. We will analyze the results of reaction-diffusion process in comparison to the front propagation methods. The contribution of different model parameters will be described by studying the development rate for resist’s de-protection level and comparing it to the development rate obtained experimentally. We will briefly discuss the results from three dimensional lithographic patterns, which exhibit strong NTD effects.
VEGF: a critical player in neurodegeneration (2004)

VEGF is a prototype angiogenic factor, but recent evidence indicates that this growth factor also has direct effects on neural cells. Abnormal regulation of VEGF expression has now been implicated in several neurodegenerative disorders, including motoneuron degeneration. This has stimulated an increasing interest in assessing the therapeutic potential of VEGF as a neuroprotective agent for such neurodegenerative disorders.
Herzinsuffizienz – Aktuelle Erfolge und Risiken der mechanischen Kreislaufunterstützung (2011)

The growing number of patients suffering from severe congestive heart failure (HF) worldwide still means a challenge for the therapeutic options, mainly in the older population. According to the rapid development in the possibilities for mechanical circulatory support (MCS), the increasing use of left ventricular assist devices (LVADs) as bridge to transplantation (BTT) or destination therapy (DT) reflects a change in the up-to-date therapy of HF. This article gives a broad overview concerning indications, patient selection, choice of the device and mainly a study update. It is clearly shown, that VAD therapy has become an effective tool in the treatment of HF, and that the modern continuous flow pumps have replaced the older, bulky, pulsatile devices, especially in the LVAD sector.