gebhart/patrepeval huggingface dataset:
Blipped‐controlled aliasing in parallel imaging for simultaneous multislice echo planar imaging with reduced <i>g</i>‐factor penalty (2011)

Simultaneous multislice Echo Planar Imaging (EPI) acquisition using parallel imaging can decrease the acquisition time for diffusion imaging and allow full-brain, high-resolution functional MRI (fMRI) acquisitions at a reduced repetition time (TR). However, the unaliasing of simultaneously acquired, closely spaced slices can be difficult, leading to a high g-factor penalty. We introduce a method to create interslice image shifts in the phase encoding direction to increase the distance between aliasing pixels. The shift between the slices is induced using sign- and amplitude-modulated slice-select gradient blips simultaneous with the EPI phase encoding blips. This achieves the desired shifts but avoids an undesired "tilted voxel" blurring artifact associated with previous methods. We validate the method in 3× slice-accelerated spin-echo and gradient-echo EPI at 3 T and 7 T using 32-channel radio frequency (RF) coil brain arrays. The Monte-Carlo simulated average g-factor penalty of the 3-fold slice-accelerated acquisition with interslice shifts is <1% at 3 T (compared with 32% without slice shift). Combining 3× slice acceleration with 2× inplane acceleration, the g-factor penalty becomes 19% at 3 T and 10% at 7 T (compared with 41% and 23% without slice shift). We demonstrate the potential of the method for accelerating diffusion imaging by comparing the fiber orientation uncertainty, where the 3-fold faster acquisition showed no noticeable degradation.
Reviving Sequential Program Birthmarking for Multithreaded Software Plagiarism Detection (2017)

As multithreaded programs become increasingly popular, plagiarism of multithreaded programs starts to plague the software industry. Although there has been tremendous progress on software plagiarism detection technology, existing dynamic birthmark approaches are applicable only to sequential programs, due to the fact that thread scheduling nondeterminism severely perturbs birthmark generation and comparison. We propose a framework called TOB (Thread-oblivious dynamic Birthmark) that revives existing techniques so they can be applied to detect plagiarism of multithreaded programs. This is achieved by thread-oblivious algorithms that shield the influence of thread schedules on executions. We have implemented a set of tools collectively called TOB-PD (TOB based Plagiarism Detection tool) by applying TOB to three existing representative dynamic birthmarks, including SCSSB (System Call Short Sequence Birthmark), DYKIS (DYnamic Key Instruction Sequence birthmark) and JB (an API based birthmark for Java). Our experiments conducted on large number of binary programs show that our approach exhibits strong resilience against state-of-the-art semantics-preserving code obfuscation techniques. Comparisons against the three existing tools SCSSB, DYKIS and JB show that the new framework is effective for plagiarism detection of multithreaded programs. The tools, the benchmarks and the experimental results are all publicly available.
Fast Optimal Resource Allocation for Scalable Video Multicast in Broadband Wireless Networks (2010)

Scalable video coding (SVC) and Adaptive Modulation and Coding (AMC) are two key techniques for video multicast in broadband wireless networks. They can improve the system performance by enhancing the wireless resource allocation schemes and assigning appropriate modulation and coding schemes (MCS) to different layers of scalable video sequences. We formulate the problem as maximizing the total system utility subject to the total resource constraint, where the utility of each user is a generic non-negative, non-decreasing function of received rate. We then propose a fast intra-session MCS assignment algorithm based on dynamic programming. This algorithm can be integrated with an existing inter-session resource allocation algorithm and applied to multi-session scenarios. Simulation results show that our algorithm achieves significant improvement on the video quality over a naive algorithm and an adapted greedy algorithm, and greatly reduces the running time in both single-session and multi-session scenarios compared to a former optimal algorithm.
Stereoselective Palladium‐Catalyzed Approach to Vitamin D<sub>3</sub> Derivatives in Protic Medium (2017)

We describe an efficient convergent synthesis of vitamin D<sub>3</sub> metabolites and analogues. The synthetic strategy relies on a tandem Pd-catalyzed A-ring closure and Suzuki-Miyaura coupling to the CD-side chain component to set directly the vitamin D triene system under protic conditions. This strategy enables rapid access to vitamin D<sub>3</sub> and 3-epi-vitamin D<sub>3</sub> metabolites and analogues modified at the side chain for biological evaluation and structural and metabolic studies.
Buffer library selection (2002)

Buffer insertion has become a critical optimization technique in high performance design. Perhaps the most prevalent buffer insertion technique is Van Ginneken's dynamic programming algorithm. Although very effective, the algorithm has time complexity that is quadratic in terms of the input buffer library size. Consequently, to achieve an efficient algorithm, it is critical that the buffer library used by the tool be relatively small, containing a subset of the most effective buffers. We propose a new algorithm for selecting a buffer library from all the buffers available in the technology, thereby permitting efficient buffer insertion. We show that the smaller buffer libraries constructed by our algorithm result in little loss in solution quality while speeding up the buffer insertion algorithm by orders of magnitude.
Novel bis-cyclic guanidines as potent membrane-active antibacterial agents with therapeutic potential (2017)

We designed a class of small dimeric cyclic guanidine derivatives which display potent antibacterial activity against both multidrug-resistant Gram-negative and Gram-positive bacteria. They could compromise bacterial membranes without developing resistance, inhibit biofilms formed by E. coli, and exhibit excellent in vivo activity in the MRSA-infected thigh burden mouse model.
A novel small molecule chaperone of rod opsin and its potential therapy for retinal degeneration (2018)

Rhodopsin homeostasis is tightly coupled to rod photoreceptor cell survival and vision. Mutations resulting in the misfolding of rhodopsin can lead to autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration that currently is untreatable. Using a cell-based high-throughput screen (HTS) to identify small molecules that can stabilize the P23H-opsin mutant, which causes most cases of adRP, we identified a novel pharmacological chaperone of rod photoreceptor opsin, YC-001. As a non-retinoid molecule, YC-001 demonstrates micromolar potency and efficacy greater than 9-cis-retinal with lower cytotoxicity. YC-001 binds to bovine rod opsin with an EC<sub>50</sub> similar to 9-cis-retinal. The chaperone activity of YC-001 is evidenced by its ability to rescue the transport of multiple rod opsin mutants in mammalian cells. YC-001 is also an inverse agonist that non-competitively antagonizes rod opsin signaling. Significantly, a single dose of YC-001 protects Abca4 <sup>-/-</sup> Rdh8 <sup>-/-</sup> mice from bright light-induced retinal degeneration, suggesting its broad therapeutic potential.
High Power Planar Sodium Metal Halide Battery (2010)

Abstract not Available.
MACROPHAGE MIGRATION INHIBITORY FACTOR IS RELEASED AS A COMPLEX WITH α1-INHIBITOR-3 IN THE INTRALUMINAL FLUID DURING BLADDER INFLAMMATION IN THE RAT (2005)

MIF is complexed with alpha1-inhibitor-3, a member of the alpha-2-macroglobulin proteinase inhibitor family, in the rat. Although SP and capsaicin increased the total amount of MIF detected by enzyme-linked immunosorbent assay in ILF, the patterns of MIF complexes elicited by these 2 treatments were different. These findings suggest that in association with other proteins MIF forms part of a complex elicited by bladder inflammation.
Polyaniline Nanofibers and Composite Materials for Chemical Detection (2005)

Recently we developed a simple, template-free chemical synthesis for polyaniline nanofibers that is selective for nanofibers, can be readily scaled to make large quantities and can be controlled to selectively produce nanofibers with narrow size distributions. Chemical sensors fabricated from polyaniline nanofibers have significantly better performance than conventional material in both sensitivity and time response. The high surface area, small diameter, and porous nature of the nanofiber films allow for facile diffusion of vapors, which is responsible for the enhanced performance. Most recently we have shown that composites with polyaniline are useful to detect analytes that do not give a significant response with unmodified polyaniline. These include fluoroalcohol additives for hydrazine detection and inorganics for hydrogen sulfide detection. Polyaniline nanofibers are superior materials that have excellent potential for many chemical detection applications.
Fibroblast Growth Factor-2 Antagonist and Antiangiogenic Activity of Long-Pentraxin 3-Derived Synthetic Peptides (2009)

Angiogenesis and inflammation are closely integrated processes. Fibroblast growth factor-2 (FGF2) is a prototypic angiogenesis inducer belonging to the family of the heparin-binding FGF growth factors. FGF2 exerts its pro-angiogenic activity by interacting with various endothelial cell surface receptors, including tyrosine kinase receptors, heparan-sulfate proteoglycans, and integrins. A tight cross-talk exists between FGF2 and the inflammatory response in the modulation of blood vessel growth. Pentraxins act as soluble pattern recognition receptors with a wide range of functions in various pathophysiological conditions. The long-pentraxin PTX3 shares the C-terminal pentraxin-domain with short-pentraxins and possesses a unique N-terminal domain. These structural features indicate that PTX3 may have distinct biological/ligand recognition properties when compared to short-pentraxins. Co-expression of PTX3 and FGF2 has been observed in different inflammation/angiogenesis-dependent diseases. PTX3 binds FGF2 with high affinity and specificity. The interaction prevents the binding of FGF2 to its cognate tyrosine kinase receptors, leading to inhibition of the angiogenic activity of the growth factor. This suggests that PTX3 may exert a modulatory function by limiting the angiogenic activity of FGF2. An integrated approach that utilized PTX3 fragments, monoclonal antibodies, and surface plasmon resonance analysis has identified the FGF2-binding domain in the unique N-terminal extension of PTX3. On this basis, PTX3-derived synthetic peptides have been designed endowed with a significant antiangiogenic activity in vitro and in vivo. They may provide the basis for the development of novel antiangiogenic FGF2 antagonists.
Non-Aqueous Ionic Liquid Energy Storage Systems (2015)

Our research has focused on the use of ionic liquids based on acetate, trifluoroacetate, hydrogen sulfate and oxalate as new types of electrolytes for non-aqueous energy storage systems. Electrodes studied have included MnO 2 , Ag 2 O, as well as Zn and Sn. Additionally, work has begun on studying the interactions of VO x electrolytes for a rechargeable V-O battery. Results will show progress towads making not only simple primary batteries, but also re chargeable systems as well. Figure 1
An Electrorheological Fluid Actuator for Rehabilitation Robotics (2018)

Transitioning rehabilitation robots from the clinic environment to the home could significantly increase the intensity and accessibility of therapy to stroke survivors. Home-based rehabilitation robots must become smaller and cheaper. In this paper, we consider a novel proof-of-concept actuator for human-machine interaction. The actuator incorporates a prototype electrorheological fluid developed to address issues previously reported in the literature. Two electrorheological fluid clutches are antagonistically arranged in a differential mechanism. The fluid clutches uncouple the output from the intrinsically high impedance of a geared dc motor. Mathematical modeling of predicted torque was compared with torque measurements. The clutches can transfer approximately 1.1 N·m at an electric field strength of 3 kV/mm. A testbed was also developed to study variable impedance control with the device where motion feedback was used to modulate the output impedance. An empirically derived model was used to program voltages/torques in response to perturbations in position. A benefit of the proposed design is the ability to statically coactivate both clutches to increase output impedance, which could potentially have benefits for training. We also discuss the advantages and disadvantages of electrorheological fluid actuators for human rehabilitation robotics.
Terahertz micromachined on-wafer probes: Repeatability and robustness (2011)

Although progress has been made in the development of submillimeter-wave monolithic integrated circuits, the evaluation of these circuits still relies on test fixtures, which makes testing expensive and time consuming. Based on a W-band prototype, a micromachined on-wafer probe covering frequencies 500-750 GHz is built to simplify submillimeter-wave integrated circuits testing. This paper demonstrates the repeatability and the robustness of this terahertz micromachined on-wafer probe.
Hyperspectral multiphoton microscopy for in vivo visualization of multiple, spectrally overlapped fluorescent labels (2020)

The insensitivity of multiphoton microscopy to optical scattering enables high-resolution, high-contrast imaging deep into tissue, including in live animals. Scattering does, however, severely limit the use of spectral dispersion techniques to improve spectral resolution. In practice, this limited spectral resolution together with the need for multiple excitation wavelengths to excite different fluorophores limits multiphoton microscopy to imaging a few, spectrally-distinct fluorescent labels at a time, restricting the complexity of biological processes that can be studied. Here, we demonstrate a hyperspectral multiphoton microscope that utilizes three different wavelength excitation sources together with multiplexed fluorescence emission detection using angle-tuned bandpass filters. This microscope maintains scattering insensitivity, while providing high enough spectral resolution on the emitted fluorescence and capitalizing on the wavelength-dependent nonlinear excitation of fluorescent dyes to enable clean separation of multiple, spectrally overlapping labels, <i>in vivo</i>. We demonstrated the utility of this instrument for spectral separation of closely-overlapped fluorophores in samples containing ten different colors of fluorescent beads, live cells expressing up to seven different fluorescent protein fusion constructs, and in multiple <i>in vivo</i> preparations in mouse cortex and inflamed skin with up to eight different cell types or tissue structures distinguished.
Abstract 5365: Prolonged survival of patients with advanced renal cancer responding to multi-peptide vaccine IMA901 after single-dose cyclophosphamide (2012)

Abstract Translational research and the clinical development of therapeutic cancer vaccines requires stronger scientific rationalization. Here we demonstrate how immune response markers as well as biomarkers defining the immune regulatory environment were utilized as guiding tools from discovery to advanced clinical trials of IMA901, a novel therapeutic vaccine for the treatment of renal cell carcinoma (RCC). IMA901 consists of multiple tumor-associated peptides (TUMAPs) confirmed to be naturally presented in human RCC tissue by mass spectrometry, selected using differential transcriptomics and preclinically validated by systematic analysis of immunogenicity with artificial antigen-presenting cells. Two consecutive independent clinical studies in a total of 96 HLA-A*02+ advanced/metastatic RCC patients were conducted. The phase I study revealed that T-cell responses to multiple IMA901 antigens were significantly associated with disease control and negatively associated with the presence of FoxP3+ regulatory T cells (Tregs). The subsequent randomized phase II study demonstrated that pre-treatment with a single low dose of cyclophosphamide (Cy) reduced Treg frequencies and prolonged overall survival (OS) in patients who mounted an immune response to the IMA901 vaccine. Additionally, T-cell responses to multiple IMA901 antigens were again associated with clinical benefit. Furthermore, a comprehensive prognostic and predictive biomarker program was conducted. Among cellular biomarkers, highly significantly elevated levels of myeloid-derived suppressor cells (MDSC), IL-17-/IL-10-secreting T cells and dysfunctional T cells in RCC patients vs. healthy individuals were found. Two MDSC populations (CD14+ HLA-DR- and CD14- CD11b+ CD15+) were significantly negatively associated with survival in vaccinated RCC patients. Interestingly, both MDSC populations were also found to be negatively associated with OS in an independent trial in colorectal cancer patients (N=79) implying a broader role for these MDSC species. Additionally, among over 300 serum biomarkers tested, apolipoprotein A-I (ApoA1) and the chemokine CCL17 were found to be predictive for both immune responses to IMA901 and survival of the RCC patients. The knowledge acquired in these trials was used to design a randomized phase III study. In this ongoing study, IMA901 is combined with the tyrosine kinase inhibitor sunitinib based on the findings that sunitinib downmodulates the two MDSC populations described above. Furthermore, in this phase III study, the relevance of ApoA1/CCL17 will be explored by prospectively defined subgroup analyses. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5365. doi:1538-7445.AM2012-5365
Autonomous Control of Pneumatically-Powered Percussive Drilling Through Highly Layered Formations (2019)

The ability to rapidly drill through diverse, layered materials can greatly enhance future mine-rescue operations, energy exploration, and underground operations. Pneumatic-percussive drilling holds great promise in this area due to its ability to penetrate very hard materials and potential for portability. Currently such systems require expert operators who require extensive training. We envision future applications where first responders who lack such training can still respond rapidly and safely perform operations. Automated techniques can reduce the dependence on expert operators while increasing efficiency and safety. However, current progress in this area is restricted by the difficulty controlling such systems and the complexity of modeling percussive rock-bit interactions. In this work we develop and experimentally validate a novel intelligent percussive drilling architecture that is tailored to autonomously operate in diverse, layered materials. Our approach combines low-level feedback control, machine learning-based material classification, and on-line optimization. Our experimental results demonstrate the effectiveness of this approach and illustrate the performance benefits over conventional methods.
Ray tracing is the future and ever will be... (2013)

The primary objective of this course is to present a coherent summary of the state of the art in ray tracing technology. The course covers the most recent developments and practical aspects of the parallel construction of acceleration data structures and traversal of such acceleration data structures using highly parallel processors, including a discussion of divergent code paths and memory accesses as well as occupancy. Ray tracing in real-time games is considered one of the main application opportunities, but an important part of the course focuses on hardware for ray tracing applications in mobile platforms.
HLA Class Ia and Ib Polyreactive Anti-HLA-E IgG2a Monoclonal Antibodies (TFL-006 and TFL-007) Suppress Anti-HLA IgG Production by CD19+ B Cells and Proliferation of CD4+ T Cells While Upregulating Tregs (2017)

The anti-HLA-E IgG2a mAbs, TFL-006 and TFL-007, reacted with all HLA-I antigens, similar to the therapeutic preparations of IVIg. Indeed, IVIg lost its HLA reactivity, when its HLA-E reactivity was adsorbed out. US-FDA approved IVIg to reduce antibodies in autoimmune diseases. But the mechanism underlying IVIg-mediated antibody reduction could not be ascertained due to the presence of other polyclonal antibodies. In spite of it, the cost prohibitive high or low IVIg is administered to patients waiting for donor organ and for allograft recipients for lowering antiallograft antibodies. A mAb that could mimic IVIg in lowering Abs, with defined mechanism of action, would be highly beneficial for patients. Demonstrably, the anti-HLA-E mAbs mimicked several functions of IVIg relevant to suppressing the antiallograft Abs. The mAbs suppressed activated T cells and anti-HLA antibody production by activated B cells, which were dose-wise superior to IVIg. The anti-HLA-E mAb expanded CD4+, CD25+, and Foxp<sup>3</sup>+ Tregs, which are known to suppress T and B cells involved in antibody production. These defined functions of the anti-HLA-E IgG2a mAbs at a level superior to IVIg encourage developing their humanized version to lower antibodies in allograft recipients, to promote graft survival, and to control autoimmune diseases.
Cofactor-Independent Pinacolase Directs Non-Diels-Alderase Biogenesis of the Brevianamides (2019)

<p>Fungal bicyclo[2.2.2]diazaoctane indole alkaloids demonstrate intriguing structures and a wide spectrum of biological activities. Although biomimetic total syntheses have been completed for representative compounds of this structural family, the details of their biogenesis have remained largely uncharacterized. Among them, Brevianamide A represents the most basic form within this class bearing a dioxopiperazine core structure and a rare 3-<i>spiro</i>-<i>psi</i>-indoxyl skeleton. Here, we identified the Brevianamide A biosynthetic gene cluster from <i>Penicillium brevicompacticum</i> NRRL 864 and fully elucidated the metabolic pathway by targeted gene disruption, heterologous expression, precursor incorporation studies, and <i>in vitro</i> biochemical analysis. In particular, we determined that BvnE is a cofactor-independent isomerase that is essential for selective production of Brevianamide A. Based on a high resolution crystal structure of BvnE, molecular modeling, mutational analysis, and computational studies provided new mechanistic insights into the diastereoselective formation of the 3-<i>spiro</i>-<i>psi</i>-indoxyl moiety in Brevianamide A. This occurs through a biocatalyst controlled semi-Pinacol rearrangement and a subsequent spontaneous intramolecular [4+2] <i>hetero</i>-Diels-Alder cycloaddition.</p>