gebhart/patrepeval huggingface dataset:
Arabidopsis ACBP1 overexpressors are Pb(II)-tolerant and accumulate Pb(II) (2008)

In our recent paper in the Plant Journal, we demonstrated that Arabidopsis thaliana acyl-CoA-binding protein ACBP1 binds lead [Pb(II)], its mRNA is induced by Pb(II)-treatment and transgenic Arabidopsis overexpressing ACBP1 are conferred Pb(II) tolerance and accumulate Pb(II). Our results suggest that ACBP1 overexpressors are potentially useful for applications in phytoremediation. Since very few plant proteins that bind and accumulate Pb(II) have been identified, our findings provide a feasible method in phytoremediating Pb(II).
Recent Advances and Future Prospects for Memristive Materials, Devices, and Systems (2023)

Memristive technology has been rapidly emerging as a potential alternative to traditional CMOS technology, which is facing fundamental limitations in its development. Since oxide-based resistive switches were demonstrated as memristors in 2008, memristive devices have garnered significant attention due to their biomimetic memory properties, which promise to significantly improve power consumption in computing applications. Here, we provide a comprehensive overview of recent advances in memristive technology, including memristive devices, theory, algorithms, architectures, and systems. In addition, we discuss research directions for various applications of memristive technology including hardware accelerators for artificial intelligence, in-sensor computing, and probabilistic computing. Finally, we provide a forward-looking perspective on the future of memristive technology, outlining the challenges and opportunities for further research and innovation in this field. By providing an up-to-date overview of the state-of-the-art in memristive technology, this review aims to inform and inspire further research in this field.
The Effect of Cyanidin-3-O-β-d-glucopyranoside on the Penile Erection and Corpus Cavernosum in a Rat Model of Diabetic Erectile Dysfunction (2011)

Purpose: The aim of this study was to evaluate Cyanidin-3-O-β-d-glucopyranoside on improvement and protection for erectile function. Materials and Methods: Sprague-Dawley rats (12wks old) were divided into three groups (n=12 in each): normal control, diabetes (DM), and diabetes with Cyanidin-3-O-β-d-glucopyranoside (C3G) concentration materials treatment (DM＋C3G). DM and DM＋C3G group received a single injection of streptozotocin (50 mg/kg), and 4 wk after induction of diabetes, DM＋C3G group were treated with daily C3G (10 mg/kg) dissolved in water for 8 wk. After 12 wk of streptozotocin injections, rats in each group underwent intracavernosal pressure measurement (ICP) and then the corporal tissues were sampled. Results: DM group showed markedly lower erectile parameters than those in the control group, whereas rats in the DM＋C3G group showed improved erectile function by minimizing corporal apoptosis. Conclusions: The current study is the first to suggest that Cyanidin-3-O-β-d-glucopyranoside may have a potency to improve and protect erectile function in a rat model of diabetic erectile dysfunction.
Customizing the Shape and Microenvironment Biochemistry of Biocompatible Macroscopic Plant-Derived Cellulose Scaffolds (2018)

Plant-derived cellulose scaffolds constitute a highly viable and interesting biomaterial. They retain a high flexibility in shape and structure, present the ability to tune surface biochemistry, display a high degree of biocompatibility, exhibit vascularization, and are widely available and easily produced. What is also immediately clear is that pre-existing cellulose structures in plants can also provide candidates for specific tissue engineering applications. Here, we report a new preparation and fabrication approach for producing large scale scaffolds with customizable macroscopic structures that support cell attachment and invasion both in vitro and in vivo. This new fabrication method significantly improves cell attachment compared to that in our previous work. Moreover, the materials remain highly biocompatible and retain vascularization properties in vivo. We present proof-of-concept studies that demonstrate how hydrogels can be temporarily or permanently cast onto the macroscopic scaffolds to create composite plant-derived cellulose biomaterials. This inverse molding approach allows us to provide temporary or permanent biochemical cues to invading cells in vitro. The development of a new-generation of rapidly and efficiently produced composite plant-derived biomaterials provides an important proof that such biomaterials have the potential for numerous applications in tissue engineering.
“Smart” Continuous Glucose Monitoring Sensors: On-Line Signal Processing Issues (2010)

The availability of continuous glucose monitoring (CGM) sensors allows development of new strategies for the treatment of diabetes. In particular, from an on-line perspective, CGM sensors can become "smart" by providing them with algorithms able to generate alerts when glucose concentration is predicted to exceed the normal range thresholds. To do so, at least four important aspects have to be considered and dealt with on-line. First, the CGM data must be accurately calibrated. Then, CGM data need to be filtered in order to enhance their signal-to-noise ratio (SNR). Thirdly, predictions of future glucose concentration should be generated with suitable modeling methodologies. Finally, generation of alerts should be done by minimizing the risk of detecting false and missing true events. For these four challenges, several techniques, with various degrees of sophistication, have been proposed in the literature and are critically reviewed in this paper.
Complexity regularized pattern matching (2009)

We propose a technique that finds optimized descriptors for pattern matching applications. We formulate the pattern matching problem as the search of a pattern library for vectors defined in a query manifold. Our approach trades off the computational complexity involved in the search with matching accuracy by representing the query manifold with its complexity-dependent approximations. This is done in an optimal way so that a user with a given complexity budget accomplishes the optimal matching performance for that budget. Our work can be seen as defining a covering around the query manifold with the aid of the derived descriptors. The higher the allowed computational complexity, the tighter the covering, and the more accurate the match. Our formulation results in sparse descriptors which naturally emerge as the optimal solutions. The proposed descriptors are adaptively optimized for the particular search problem so that application-specific simplifications are taken full advantage of. Thanks to our algebraic approach, the presented formulation is general and can readily be applied to many different types of signals in addition to images and video.
Program for Analyzing Flows in a Complex Network (2006)

Generalized Fluid System Simulation Program (GFSSP) version 4 is a general-purpose computer program for analyzing steady-state and transient flows in a complex fluid network. The program is capable of modeling compressibility, fluid transients (e.g., water hammers), phase changes, mixtures of chemical species, and such externally applied body forces as gravitational and centrifugal ones. A graphical user interface enables the user to interactively develop a simulation of a fluid network consisting of nodes and branches. The user can also run the simulation and view the results in the interface. The system of equations for conservation of mass, energy, chemical species, and momentum is solved numerically by a combination of the Newton-Raphson and successive-substitution methods.
Recovery of Uranium from Seawater: A Review of Current Status and Future Research Needs (2013)

The recovery of uranium (U) from seawater has been investigated for over six decades in efforts to secure uranium sources for future energy production. The majority of the research activities have focused on inorganic materials, chelating polymers, and nanomaterials. Previous studies of uranium adsorption from aqueous solutions, mainly seawater, are reviewed here with a focus on various adsorbent materials, adsorption parameters, adsorption characterization, and marine studies. Continuous progress has been made over several decades, with adsorbent loadings approaching 3.2 mg U/g adsorbent in equilibrium with seawater. Further research is needed to improve first, the viability including improved capacity, selectivity, and kinetics, and second, the sorbent regeneration for multicycle use. An overview of the status of the uranium adsorption technology is provided and future research needs to make this technology commercially competitive are discussed.
Ultra-slim coherent backlight unit for mobile holographic display (2015)

We propose slim coherent backlight unit for a mobile holographic display. This backlight unit consists of glass substrate for waveguide and two surface gratings produced by two-beam interference. The area of backlight illumination is 150 by 85 mm, and the thickness is 0.7 mm, which is thin compared to other conventional coherent backlight units. This backlight unit exhibits a total efficiency of 0.1%, preserving the collimation and a uniformity of 80% over the whole area. The proposed slim coherent backlight can be applied to a mobile holographic display.
Discovery and optimization of a novel anti-GUCY2c x CD3 bispecific antibody for the treatment of solid tumors (2021)

We report here the discovery and optimization of a novel T cell retargeting anti-GUCY2C x anti-CD3ε bispecific antibody for the treatment of solid tumors. Using a combination of hybridoma, phage display and rational design protein engineering, we have developed a fully humanized and manufacturable CD3 bispecific antibody that demonstrates favorable pharmacokinetic properties and potent <i>in vivo</i> efficacy. Anti-GUCY2C and anti-CD3ε antibodies derived from mouse hybridomas were first humanized into well-behaved human variable region frameworks with full retention of binding and T-cell mediated cytotoxic activity. To address potential manufacturability concerns, multiple approaches were taken in parallel to optimize and de-risk the two antibody variable regions. These approaches included structure-guided rational mutagenesis and phage display-based optimization, focusing on improving stability, reducing polyreactivity and self-association potential, removing chemical liabilities and proteolytic cleavage sites, and de-risking immunogenicity. Employing rapid library construction methods as well as automated phage display and high-throughput protein production workflows enabled efficient generation of an optimized bispecific antibody with desirable manufacturability properties, high stability, and low nonspecific binding. Proteolytic cleavage and deamidation in complementarity-determining regions were also successfully addressed. Collectively, these improvements translated to a molecule with potent single-agent <i>in vivo</i> efficacy in a tumor cell line adoptive transfer model and a cynomolgus monkey pharmacokinetic profile (half-life>4.5 days) suitable for clinical development. Clinical evaluation of PF-07062119 is ongoing.
Ceramic Laser Materials (2012)

Ceramic laser materials have come a long way since the first demonstration of lasing in 1964. Improvements in powder synthesis and ceramic sintering as well as novel ideas have led to notable achievements. These include the first Nd:yttrium aluminum garnet (YAG) ceramic laser in 1995, breaking the 1 KW mark in 2002 and then the remarkable demonstration of more than 100 KW output power from a YAG ceramic laser system in 2009. Additional developments have included highly doped microchip lasers, ultrashort pulse lasers, novel materials such as sesquioxides, fluoride ceramic lasers, selenide ceramic lasers in the 2 to 3 μm region, composite ceramic lasers for better thermal management, and single crystal lasers derived from polycrystalline ceramics. This paper highlights some of these notable achievements.
Inhibition of thyrotropin binding to receptor by synthetic human thyrotropin beta peptides. (1990)

In order to study the structure and function relationships of the thyrotropin (TSH)-specific beta-subunit, we produced 11 synthetic overlapping peptides containing the entire 112-amino acid sequence of human beta TSH and tested them for activity in TSH radioreceptor assay using both human and porcine thyroid membranes. Synthetic peptides representing four regions of the beta-subunit demonstrated the ability to inhibit binding of 125I-bovine TSH to crude thyroid membranes. The peptide representing the -COOH terminus of the subunit (beta 101-112) possessed highest binding activity, inhibiting binding of labeled TSH with an EC50 of 80 microM. The remaining active peptides were: beta 71-85 (104 microM), beta 31-45 (186 microM), beta 41-55 (242 microM), and beta 1-15 (331 microM). Specificity of the binding activity was shown by the inability of the peptides representing the remainder of the subunit to inhibit binding of label and by the inability of any of the peptides to inhibit binding of 125I-epidermal growth factor to the same thyroid membranes. The low affinity of the peptides as compared with native hormone is in agreement with previous studies of synthetic alpha-subunit peptides and, further, suggests that the interaction of beta TSH with receptor is multifaceted, requiring cooperative binding of these sites for the observed high affinity of the whole hormone. These studies are in agreement with previous predictions of active regions by chemical modification but add two regions to the list, showing the utility of the synthetic peptide strategy in the study of peptide hormone structure-activity relationships.
Incremental high-level synthesis (2010)

The widespread acceptance of High-level synthesis as a mainstream tool mostly depends on its tight integration with the following RTL-to-GDSII design flow. A key aspect is the handling of so-called Engineering Change Orders (ECOs), i.e. minor changes required to fix small functional bugs or meet performance requirements late in the design cycle. Traditional high-level synthesis has attempted to optimize at best the output logic. However, in the ECO scenario the goal is to implement the required change with as few modifications as possible to the RTL, logic netlist, placed netlist and layout. In this paper we show how, by judiciously changing the internal databases used by the tool to match as much as possible the original design, one can achieve minimal impact and implement ECOs in truly incremental mode, while full-blow re-synthesis would lead to massive unnecessary downstream changes. The tool essentially matches source constructs between the original and the ECO design, and copies as many synthesis decisions as possible from the original design to the ECO design.
Exploring Spacer Arm Structures for Designs of Asymmetric Sulfoxide-Containing MS-Cleavable Cross-Linkers (2020)

Cross-linking mass spectrometry (XL-MS) has become a powerful structural tool for defining protein-protein interactions (PPIs) and elucidating architectures of large protein assemblies. To advance XL-MS studies, we have previously developed a series of sulfoxide-containing MS-cleavable cross-linkers to facilitate the detection and identification of cross-linked peptides using multistage mass spectrometry (MS<sup><i>n</i></sup>). While current sulfoxide-based cross-linkers are effective for in vivo and in vitro XL-MS studies at the systems-level, new reagents are still needed to help expand PPI coverage. To this end, we have designed and synthesized six variable-length derivatives of disuccinimidyl sulfoxide (DSSO) to better understand the effects of spacer arm modulation on MS-cleavability, fragmentation characteristics, and MS identification of cross-linked peptides. In addition, the impact on cross-linking reactivity was evaluated. Moreover, alternative MS<sup>2</sup>-based workflows were explored to determine their feasibility for analyzing new sulfoxide-containing cross-linked products. Based on the results of synthetic peptides and a model protein, we have further demonstrated the robustness and predictability of sulfoxide chemistry in designing MS-cleavable cross-linkers. Importantly, we have identified a unique asymmetric design that exhibits preferential fragmentation of cross-links over peptide backbones, a desired feature for MS<sup><i>n</i></sup> analysis. This work has established a solid foundation for further development of sulfoxide-containing MS-cleavable cross-linkers with new functionalities.
Identification of the Tuberous Sclerosis Gene <i>TSC1</i> on Chromosome 9q34 (1997)

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the widespread development of distinctive tumors termed hamartomas. TSC-determining loci have been mapped to chromosomes 9q34 (TSC1) and 16p13 (TSC2). The TSC1 gene was identified from a 900-kilobase region containing at least 30 genes. The 8.6-kilobase TSC1 transcript is widely expressed and encodes a protein of 130 kilodaltons (hamartin) that has homology to a putative yeast protein of unknown function. Thirty-two distinct mutations were identified in TSC1, 30 of which were truncating, and a single mutation (2105delAAAG) was seen in six apparently unrelated patients. In one of these six, a somatic mutation in the wild-type allele was found in a TSC-associated renal carcinoma, which suggests that hamartin acts as a tumor suppressor.
Antifungal amphiphilic kanamycins: new life for an old drug (2018)

Classical aminoglycoside antibiotics are obsolete or hampered by the emergence of drug resistant bacteria. Recent discoveries of antifungal amphiphilic kanamycins offer new strategies for reviving and repurposing these old drugs. A simple structural modification turns the clinically obsolete antibacterial kanamycin into an antifungal agent. Structure-activity relationship studies have led to the production of <b>K20</b>, an antifungal kanamycin that can be mass-produced for uses in agriculture as well as in animals. This review delineates the path to the discovery of <b>K20</b> and other related antifungal amphiphilic kanamycins, determination of its mode of action, and findings in greenhouse and field trials with <b>K20</b> that could lead to crop disease protection strategies.
A Distributed Inter-Cell Interference Coordination Scheme between Femtocells in LTE-Advanced Networks (2011)

Due to the dense and self-deployment of home eNodeBs (HeNBs) in femtocells, serious inter-cell interference may arise without good coordination. To deal with it, a distributed interference coordination scheme for femtocells networks with carrier aggregation (CA) is proposed in this paper. Firstly, each femtocell operates on all the component carriers (CCs) of the network and gathers the information needed via local measurements. Then, based on the measurements, decisions of maintaining or releasing the component carrier are individually made by each femtocell on each component carrier. Simulation results validate the effectiveness of our proposed scheme in term of the signal to interference and noise ratio (SINR) and throughput.
ChemInform Abstract: Structure—Activity Relationships of Stemphones, Potentiators of Imipenem Activity Against Methicillin‐Resistant Staphylococcus aureus. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Bioactive material template for <i>in vitro</i>, synthesis of bone (1995)

We describe the synthesis of a new, porous, modified bioactive glass for use as a template for bone formation in vitro. The porosity of the glass was 36.4%; the pore size ranged from 10-160 mm, and there was no incipient devitrification. Prior to seeding the glass with cells, it was necessary to condition the disks. Optimum conditioning was achieved by immersing the templates in a tris buffer at pH 6.8 for 48 h and then treating the glass with tissue culture medium for 1 h at 37 degrees C. The conditioned glass disks were seeded with 10(6) neonatal rat calvaria osteoblast-like cells; cells on the substrate were maintained in culture for 3-7 days. To prevent pH shifts due to corrosion of the conditioned glass, the medium:glass ratio was maintained at 90 ml/g. We found that the templates were rapidly invaded by cells which maintained the osteoblast phenotype; thus, they exhibited high alkaline phosphatase activity and synthesized type I collagen and osteocalcin. SEM-EDAX showed that the cells elaborated substantial amounts of extracellular matrix and a bonelike tissue was present throughout the entire template thickness. FTIR analysis of material formed in the glass indicated that the mineral phase was a biologic hydroxyapatite. Controls (cells without substrate and substrate without cells) exhibited none of these features. Results of the study suggest that this porous glass can function as a template for generating bone in vitro.
Discovery of piperidine-substituted thiazolo[5,4-d]pyrimidine derivatives as potent and orally bioavailable HIV-1 non-nucleoside reverse transcriptase inhibitors (2019)

Abstract HIV-1 reverse transcriptase offers a key target for antiviral therapy. However, the rapid emergence of drug-resistant mutations in reverse transcriptase as well as the poor pharmacokinetic properties of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) limits their clinical use. Starting from a previous piperidine-substituted thiophene[3,2- d ]pyrimidine compound (K-5a2), here we explore the chemical space around the thiophene ring located in the solvent-exposed regions of the NNRTI binding pocket in detail. Bioisosterism-based structural modification leads to the discovery of a number of compounds as potent in vitro reverse transcriptase inhibitors, providing improved drug resistance profiles compared to the listed drug Etravirine. Furthermore, 14a and 19a are identified as lead compounds with good solubility, appropriate ligand efficiency, and lower cytochrome P450 liability. Compound 19a exhibits useful in vivo pharmacokinetic properties in rat and safety in mice, suggesting that it may have the potential to be an effective drug candidate for treating AIDS.
<title>Augmented-reality visualization in iMRI operating room: system description and preclinical testing</title> (2002)

We developed an augmented reality system targeting image guidance for surgical procedures. The surgeon wears a video- see-through head mounted display that provides him with a stereo video view of the patient. The live video images are augmented with graphical representations of anatomical structures that are segmented from medical image data. The surgeon can see, e.g., a tumor in its actual location inside the patient. This in-situ visualization, where the computer maps the image information onto the patient, promises the most direct, intuitive guidance for surgical procedures. In this paper, we describe technical details of the system and its installation in UCLA's iMRI operating room. We added instrument tracking to the capabilities of our system to prepare it for minimally invasive procedures. We discuss several pre-clinical phantom experiments that support the potential clinical usefulness of augmented reality guidance.